Townships, the International City/County Management Association, and
the Environmental Council of States. In addition, the National
Association of Clean Water Agencies (NACWA) and the Association of
Clean Water Administrators (ACWA) were invited to participate. As part
of the consultation 12 counties, 8 associations and various state
agencies and offices from five states (Alaska, Wyoming, Kansas,
Tennessee, and Texas) submitted written comments. In addition, EPA held
numerous outreach calls with state and local government agencies
seeking their technical input. More than 400 people from a variety of
state and local agencies and associations, including the Western
Governors' Association, the Western States Water Council and the
Association of State Wetland Managers participated in various calls and
meetings.
    The agencies engaged in voluntary federalism consultation on this
rule and we will continue to work closely with the states with respect
to development of a final rule. Additionally, EPA and the Corps are
specifically soliciting comments on this proposed action from state and
local officials. The agencies will include a detailed narrative of
intergovernmental concerns raised during the course of the rule's
development and a description of the agencies' efforts to address them
with the final rule.

F. Executive Order 13175: Consultation and Coordination With Indian
Tribal Governments

    Subject to the Executive Order (E.O.) 13175 (65 FR 67249, November
9, 2000) Agencies may not issue a regulation that has tribal
implications, that imposes substantial direct compliance costs, and
that is not required by statute, unless the Federal government provides
the funds necessary to pay the direct compliance costs incurred by
tribal governments, or the Agencies consult with tribal officials early
in the process of developing the proposed regulation and develops a
tribal summary impact statement. This action does not have tribal
implications as specified in E.O. 13175.
    In compliance with the EPA Policy on Consultation and Coordination
with Indian Tribes (May 4, 2011), EPA consulted with tribal officials
to gain an understanding of and, where appropriate, to address the
tribal implications of the proposed rule. In the course of this
consultation EPA coordinated with the Corps, and the Corps jointly
participated in aspects of the consultation process. In the fall of
2011 EPA sent a Tribal Consultation Notification letter to all
federally-recognized tribal leaders, via mail and email, inviting
tribal officials to participate in outreach and consultation events and
provide comments to EPA in coordination with the Corps. Close to 200
tribal representatives and more than 40 tribes participated in the
consultation process, which included multiple webinars and national
teleconferences and face-to-face meetings. In addition, EPA received
written comments from 3 tribes during the consultation period. In the
spirit of E.O. 13175, and consistent with EPA and Corps policy to
promote communications between the agencies and tribal governments, the
agencies specifically solicit additional comment on this proposed
action from tribal officials.

G. Executive Order 13045: Protection of Children From Environmental
Health and Safety Risks

    This action is not subject to E.O. 13045 because the environmental
health or safety risks addressed by this action do not present a
disproportionate risk to children.

H. Executive Order 13211: Actions Concerning Regulations That
Significantly Affect Energy Supply, Distribution, or Use

    This action is not a ``significant energy action'' as defined in
Executive Order 13211 (66 FR 28355, May 22, 2001), because it is not
likely to have a significant adverse effect on the supply,
distribution, or use of energy.

I. National Technology Transfer and Advancement Act

    Section 12(d) of the National Technology Transfer and Advancement
Act of 1995 (``NTTAA''), Public Law 104-113, 12(d) (15 U.S.C. 272 note)
directs Federal agencies to use voluntary consensus standards in its
regulatory activities unless to do so would be inconsistent with
applicable law or otherwise impractical. Voluntary consensus standards
are technical standards (e.g., materials specifications, test methods,
sampling procedures, and business practices) that are developed or
adopted by voluntary consensus standards bodies. NTTAA directs Federal
agencies to provide Congress, through OMB, explanations when the Agency
decides not to use available and applicable voluntary consensus
standards.
    This proposed rulemaking does not involve technical standards.
Therefore, the agencies are not considering the use of any voluntary
consensus standards.

J. Executive Order 12898: Federal Actions To Address Environmental
Justice in Minority Populations and Low-Income Populations

    Executive Order (E.O.) 12898 (59 FR 7629, Feb. 16, 1994)
establishes Federal executive policy on environmental justice. Its main
provision directs Federal agencies, to the greatest extent practicable
and permitted by law, to make environmental justice part of their
mission by identifying and addressing, as appropriate,
disproportionately high and adverse human health or environmental
effects of their programs, policies, and activities on minority
populations and low-income populations in the United States.
    The agencies have determined that this proposed rule will not have
disproportionately high and adverse human health or environmental
effects on minority or low-income populations. The proposed rule
defines the scope of waters protected under the CWA. The increased
clarity regarding the definition of ``waters of the United States''
will be of benefit to all regulators, stakeholders, and interested
parties. However, in the spirit of Executive Order 12898, we
specifically request comment regarding potential environmental justice
issues raised by the proposed rule, and will fully consider those
comments when preparing the final rule.

K. Environmental Documentation

    The U.S. Army Corps of Engineers has prepared a draft environmental
assessment in accordance with the National Environmental Policy Act
(NEPA). The Corps has made a preliminary determination that the section
404 aspects of today's proposed rule do not constitute a major Federal
action significantly affecting the quality of the human environment,
and thus preparation of an Environmental Impact Statement (EIS) will
not be required. The proposed rule will increase and make more
efficient the protection of the aquatic environment. Additionally, the
Corps complies with NEPA programmatically for general permits, and
specifically for each and every standard individual permit application
before making final permit decisions.
    The implementation of the procedures prescribed in this proposed
regulation would not authorize anyone (e.g., any landowner or permit
applicant) to perform any work involving regulated activities in
``waters of the United States'' without first seeking and obtaining an
appropriate CWA authorization, which concurrently documents compliance
with all applicable environmental laws.

Appendix A

Scientific Evidence

Overview of Scientific Literature on Aquatic Resource Connectivity and
Downstream Effects

    In preparation for this proposal, more than a thousand peer-
reviewed scientific papers and other data that address connectivity
of aquatic resources and effects on downstream waters were reviewed
and considered. EPA's Office of Research and Development (ORD) has
prepared a draft peer-reviewed synthesis of published peer-reviewed
scientific literature discussing the nature of connectivity and
effects of tributaries and wetlands on downstream waters (U.S.
Environmental Protection Agency, Connectivity of Streams and
Wetlands to Downstream Waters: A Review and Synthesis of the
Scientific Evidence, (Washington, DC: U.S. Environmental Protection
Agency, 2013), hereinafter, ``Report''). This draft Report similarly
has been considered in the development of this proposal. The Report
is currently undergoing peer review led by EPA's Scientific Advisory
Board (SAB) and is available at http://yosemite.epa.gov/sab/sabproduct.nsf/fedrgstr_activites/Watershed%20Connectivity%20Report?OpenDocument. The Report also
underwent an earlier peer review, and the results of this peer
review are available in the docket for this proposed rule. The
Report summarizes and assesses much of the currently available
scientific literature that is part of the administrative record for
this proposal. The agencies anticipate that additional data and
information will become available during the rulemaking process,
including that provided during the public comment process, and by
additional research, studies, and investigations that take place
before the rulemaking process is concluded. At the conclusion of the
rulemaking process, the agencies will review the entirety of the
completed administrative record, including the final Report
reflecting SAB review, and will make any adjustments to the final
rule deemed to be appropriate at that time. The Report is under
review by the Science Advisory Board, and the rule will not be
finalized until that review and the final report are complete. Part
I of this Appendix provides the conclusions of the review and
synthesis. Part II provides additional detail of the scientific
literature and the agencies' reasoning in support of this proposal.

Part I: Synthesis of Peer-Reviewed Scientific Literature

Background

    The draft Report prepared by ORD reviews and synthesizes the
peer-reviewed scientific literature on the connectivity or isolation
of streams and wetlands relative to large water bodies such as
rivers, lakes, estuaries, and oceans. The purpose of the review and
synthesis is to summarize current understanding about these
connections, the factors that influence them, and the mechanisms by
which connected waters, singly or in aggregate, affect the function
or condition of downstream waters. The focus of the Report is on
surface and shallow subsurface connections from small or temporary
streams, non-tidal wetlands, and certain open waters. Specific types
of connections considered in the Report include transport of
physical materials and chemicals such as water, wood, and sediment,
nutrients, pesticides, and mercury; movement of organisms or their
seeds or eggs; and hydrologic and biogeochemical interactions
occurring in surface and groundwater flows, including hyporheic
zones and alluvial aquifers.
    The draft Report prepared by ORD consists of six chapters.
Following an executive summary and an introduction to the Report,
chapter 3 presents a conceptual framework describing the hydrologic
elements of a watershed, the types of chemical, physical, and
biological connections that link them, and watershed and climatic
factors that influence connectivity at various temporal and spatial
scales. It also provides background on the structure and function of
streams and wetlands viewed from an integrated watershed
perspective. In a discussion of connectivity, the watershed scale is
the appropriate context for interpreting technical evidence about
individual watershed components, reviewed in subsequent chapters.
Chapter 4 surveys the literature on stream networks (lotic systems)
in terms of chemical, physical, and biological connections between
upstream and downstream habitats. Two case studies from the
literature examine in greater detail longitudinal connectivity and
downstream effects in prairie streams and arid streams of the
Southwest. Chapter 5 reviews the literature on connectivity and
effects of non-tidal wetlands and certain open waters (lentic
systems) on downstream waters. This chapter is further subdivided
into two broad categories of landscape settings based on
directionality of hydrologic flows: Bidirectional settings, in which
wetlands and open waters can have two-way hydrologic exchanges with
other water bodies (e.g., riparian and floodplain wetlands and open
waters), and unidirectional settings, in which water flows only from
the wetland or open water towards the downstream water (e.g., most
wetlands and open waters outside of riparian areas and floodplains).
Directionality of hydrologic flow was selected as an organizational
principle for this section because it has a dominant role in
determining the types of connectivity and downstream effects (if
any) of wetlands. However, the use of these landscape settings for
hydrologic directionality should not be construed as suggesting
directionality of geochemical or biological flows. Also, the terms
``unidirectional'' and ``bidirectional'' describe the landscape
setting in which wetlands and open waters occur, and do not refer to
wetland type or class. Four case studies from the literature examine
evidence pertaining to connectivity and downstream effects of oxbow
lakes, Carolina and Delmarva bays, prairie potholes, and vernal
pools in greater detail.
    Chapter 6 presents and discusses key findings and major
conclusions of the review, which also are included at the end of
each review section and in this executive summary.

Summary of Major Conclusions

    Based on the review and synthesis of more than a thousand
publications from the peer-reviewed scientific literature, the
available evidence supports three major conclusions:
    1. The scientific literature demonstrates that streams,
individually and cumulatively, exert a strong influence on the
character and functioning of downstream waters. All tributary
streams, including perennial, intermittent, and ephemeral streams,
are chemically, physically, and biologically connected to downstream
rivers via channels and associated alluvial deposits where water and
other materials are concentrated, mixed, transformed, and
transported. Headwater streams (headwaters) are the most abundant
stream-type in most river networks, and supply most of the water in
rivers. In addition to water, streams supply sediment, wood, organic
matter, nutrients, chemical contaminants, and many of the organisms
found in rivers. Streams are biologically connected to downstream
waters by the dispersal and migration of aquatic and semi-aquatic
organisms, including fish, amphibians, plants, microorganisms, and
invertebrates, that use both up- and downstream habitats during one
or more stages of their life cycles, or provide food resources to
downstream communities. Chemical, physical, and biological
connections between streams and downstream waters interact via
processes such as nutrient spiraling, in which stream communities
assimilate and chemically transform large quantities of nitrogen and
other nutrients that would otherwise increase nutrient loading
downstream.

    2. Wetlands and open waters in landscape settings that have
bidirectional hydrologic exchanges with streams or rivers (e.g.,
wetlands and open waters in riparian areas and floodplains) are
chemically, physically, and biologically connected with rivers via
the export of channel-forming sediment and woody debris, temporary
storage of local groundwater that supports baseflow in rivers, and
transport of stored organic matter. They remove and transform excess
nutrients such as nitrogen and phosphorus. They provide nursery
habitat for breeding fish, colonization opportunities for stream
invertebrates, and maturation habitat for stream insects. Moreover,
wetlands in this landscape setting serve an important role in the
integrity of downstream waters because they also act as sinks by
retaining floodwaters, sediment, nutrients, and contaminants that
could otherwise negatively impact the condition or function of
downstream waters.
    3. Wetlands and open waters in landscape settings that lack
bidirectional hydrologic exchanges with downstream waters (e.g.,
many prairie potholes, vernal pools, and playa lakes) provide
numerous functions that can benefit downstream water quality and
integrity. These functions include storage of floodwater; retention
and transformation of nutrients, metals, and pesticides; and re-
charge of groundwater sources of river baseflow. The functions and
effects of this diverse group of wetlands, which the Report refers
to as ``unidirectional wetlands,'' affect the condition of
downstream waters if there is a surface or shallow subsurface water
connection to the river network. In unidirectional wetlands that are
not connected to the river network through surface or shallow
subsurface water, the type and degree of connectivity varies
geographically within a watershed and over time. Because such
wetlands occur on a gradient of connectivity, it is difficult to
generalize about their effects on downstream waters. Generalization
for this class is further complicated because, for certain functions
(e.g., sediment removal and water storage), downstream effects are
due to wetland isolation, rather than connectivity. The literature
reviewed does not provide sufficient information to evaluate or
generalize about the degree of connectivity (absolute or relative)
or the downstream effects of wetlands in unidirectional landscape
settings. However, evaluations of individual geographically isolated
wetlands or groups of geographically isolated wetlands could be
possible through case-by-case analysis. Further, while the review
did not specifically address other unidirectional water bodies, the
conclusions apply to these water bodies (e.g., ponds and lakes that
lack surface water inlets) as well, since the same principles govern
hydrologic connectivity between these water bodies and downstream
waters.
    Section 3 below provides an overview of the conceptual
framework, with further discussion of the key findings for streams,
riparian and floodplain areas, and unidirectional wetlands.

1. Conceptual Framework Overview

    Connectivity is a foundational concept in hydrology and
freshwater ecology. The structure and function of downstream waters
are highly dependent on the constituent materials contributed by and
transported through water bodies located elsewhere in the watershed.
Most of the materials in a river, including water, sediment, wood,
organic matter, nutrients, chemical contaminants, and certain
organisms, originate outside of the river, from upstream
tributaries, wetlands, or other components of the river system, and
are transported to the river by water movement, wind, or other
means. Therefore, streams and wetlands fundamentally affect river
structure and function by altering transport of various types of
materials to the river. This alteration of material transport
depends on two key factors: (1) Connectivity (or isolation) between
streams, wetlands and rivers that enables (or prevents) the movement
of materials between the system components; and (2) functions within
streams and wetlands that supply, remove, transform, provide refuge
for, or delay transport of materials.
    The ORD Report defines connectivity as the degree to which
components of a system are joined, or connected, by various
transport mechanisms. Connectivity is determined by the
characteristics of both the physical landscape and the biota of the
specific system. Isolation is the opposite of connectivity; or the
degree to which system components are not joined. Both connectivity
and isolation have important effects on downstream waters. For
example, stream channels convey water and channel-forming sediment
to rivers, whereas wetlands that lack output channels can reduce
flooding and store excess sediment. Materials transport connects
different ecosystem types, at multiple spatial and temporal scales.
For example, streams flowing into and out of wetlands or between
lakes form continuous or seasonal connections across ecosystem
boundaries. Similarly, aquatic food webs connect terrestrial
ecosystems, streams, wetlands, and downstream waters.
    Water movement through the river system is the primary, but
certainly not the only, mechanism providing physical connectivity
within river networks. It provides a ``hydraulic highway'' that
transports chemical, physical, and biological materials associated
with the water (e.g., sediment, woody debris, contaminants, and
organisms). Because the movement of water is fundamental to
understanding watershed connectivity, Chapter 3 begins with a review
and an explanation of the hydrologic foundation of river systems,
and terms and concepts used throughout the Report are defined.
    Numerous factors influence watershed connectivity. Climate,
watershed topography, soil and aquifer permeability, the number and
types of contributing waters, their spatial distribution in the
watershed, interactions among aquatic organisms, and human
alteration of watershed features, among other things, can act
individually or in concert to influence stream and wetland
connectivity to, and effects on, downstream waters. For example, all
else being equal, materials traveling shorter distances could enter
the river with less transformation or dilution, thus increasing a
beneficial or harmful effect. In other cases, sequential
transformations such as nutrient spiraling (defined and discussed
below) connect distant water bodies and produce beneficial effects
on downstream waters. Infrequent events that temporarily connect
nearby or distant streams or wetlands to rivers also can have large,
long-lasting effects. Most of the major changes in sediment load and
river channel structure that are critical to maintaining river
health--including meanders of rivers in floodplains and creation of
oxbow lakes--are a result of large floods that provide infrequent,
intense connections with more distant streams and riparian or
floodplain waters.
    Based on a review of the peer-reviewed scientific literature,
the Report identifies five functions by which streams, wetlands, and
open waters influence material transport into downstream waters:

 Source: The net export of materials, such as water and food
resources
 Sink: The net removal or storage of materials, such as
sediment and contaminants
 Refuge: The protection of materials, especially organisms
 Transformation: The transformation of materials, especially
nutrients and chemical contaminants, into different physical or
chemical forms
 Lags: The delayed or regulated release of materials, such
as storm water

    These functions are not static or mutually exclusive (e.g., a
wetland can be both a source of organic matter and a sink for
nitrogen) and can change over time (e.g., one wetland can be a water
sink when evapotranspiration is high and a water source when
evapotranspiration is low). Further, some functions work in
conjunction with others. For example, a lag function can include
transformation of materials prior to their delayed release. In a
particular stream, wetland, or open water, the presence or absence
of these functions depends upon the biota, hydrology, and
environmental conditions in the watershed.
    When considering effects on downstream waters, it is helpful to
distinguish between actual function and potential function of a
stream, wetland, or open water. For example, a wetland with
appropriate conditions for denitrification is a potential sink for
nitrogen, a nutrient that can be a contaminant when present in high
concentrations. This function is conditional; if nitrogen were to
enter a wetland (from agricultural runoff, for example), the wetland
has the capacity to remove this nitrogen from the water. The wetland
will not serve this function, however, if no nitrogen enters the
wetland. Even if a stream or wetland is not currently serving an
actual function, it has the potential to provide that function when
a new material enters it, or when environmental conditions change.
Thus, potential functions play a critical role in protecting those
waters from future impacts.

2. Discussion of Major Conclusions

A. Streams

    The scientific literature demonstrates that streams,
individually or cumulatively, exert a strong influence on the
character and functioning of downstream waters. All tributary
streams, including perennial, intermittent, and ephemeral streams,
are chemically, physically, or biologically connected to downstream
rivers via channels and associated alluvial deposits where water and
other materials are concentrated, mixed, transformed, and
transported. Headwater streams (headwaters) are the most abundant
stream type in most river networks, and supply most of the water in
rivers. In addition to water, streams supply sediment, wood, organic
matter, nutrients, chemical contaminants, and many of the organisms
found in rivers. Streams are biologically connected to downstream
waters by dispersal and migration of aquatic and semi-aquatic
organisms, including fish, amphibians, plants, microorganisms, and
invertebrates, that use both up- and downstream habitats during one
or more stages of their life cycles, or provide food resources to
downstream communities. Chemical, physical, and biological
connections between streams and downstream waters interact via
processes such as nutrient spiraling, in which stream communities
assimilate and chemically transform large quantities of nitrogen and
other nutrients that would otherwise increase nutrient loading
downstream.
    Key findings:
    a. Streams are hydrologically connected to downstream waters via
channels that convey surface and subsurface water year-round
(perennial flow), weekly to seasonally (intermittent flow), or only
in direct response to precipitation (ephemeral flow). Streams are
the dominant source of water in most rivers, and the great majority
of tributaries are perennial, intermittent, and ephemeral headwater
streams. For example, headwater streams, which are the smallest
channels where stream flows begin, are the source of approximately
60% of the total mean annual flow to all northeastern U.S. streams
and rivers.
    b. Headwaters convey water into local storage compartments such
as ponds, shallow aquifers, or river banks and into regional and
alluvial aquifers. These local storage compartments are important
sources of water for baseflow in rivers. The ability of streams to
keep flowing even during dry periods typically depends on the
delayed (lagged) release of local groundwater, also referred to as
shallow groundwater, originating from these water sources,
especially in areas with shallow groundwater tables and pervious
subsurfaces. For example, in the southwestern United States, short-
term shallow groundwater storage in alluvial floodplain aquifers,
with gradual release into stream channels by intermittent and
ephemeral streams, is a major source of annual flow in rivers.
    c. Even infrequent flows through ephemeral or intermittent
channels influence fundamental biogeochemical processes by
connecting the channel and shallow groundwater with other landscape
elements. Infrequent, high-magnitude events are especially important
for transmitting materials from headwater streams in most river
networks. For example, headwater streams, including ephemeral and
intermittent streams, shape river channels by accumulating and
gradually or episodically releasing stored materials such as
sediment and large woody debris. These materials provide substrate,
habitat for aquatic organisms, and slow the flow of water through
channels.
    d. Connectivity between streams and rivers provides
opportunities for materials, including nutrients and chemical
contaminants, to be sequentially altered as they are transported
downstream. Although highly efficient at transport of water and
other physical materials, streams are not pipes. They are dynamic
ecosystems with permeable beds and banks that interact with
terrestrial and aquatic ecosystems above and below the surface. The
connections formed by surface and subsurface streamflows act as a
series of complex chemical, physical, and biological alterations
that occur as materials move through different parts of the river
system. The amount and quality of such materials that eventually
reach a river are determined by the aggregate effect of these
sequential alterations that begin at the source waters, which can be
at some distance from the river. The greater the distance a material
travels between a particular stream reach and the river, the greater
the opportunity for that material to be altered in intervening
stream reaches, which can allow for uptake, assimilation, or
beneficial transformation. One example of sequential alteration with
significant beneficial effects on downstream waters is the process
of nutrient spiraling, in which nutrients entering headwater streams
are transformed by various aquatic organisms and chemical reactions
as they are transported downstream by streamflow. Nutrients which
enter the headwater stream (e.g., via overland flow) are first
removed from the water column by streambed algal and microbial
populations. Fish or insects feeding on algae and microbes take up
some of those nutrients, which are subsequently released back to the
stream via excretion and decomposition, and the cycle is repeated.
In each phase of the cycling process--from dissolved inorganic
nutrients in the water column, through microbial uptake, subsequent
transformations through the food web, and back to dissolved
nutrients in the water column--nutrients are subject to downstream
transport. Stream and wetland capacities for nutrient cycling have
important implications for the form and concentration of nutrients
exported to downstream waters.
    e. The literature review found strong evidence that headwater
streams function as nitrogen sources (export) and sinks (uptake and
transformation) for river networks. One study estimated that rapid
nutrient cycling in small streams that were free from agricultural
or urban impacts removed 20-40% of the nitrogen that otherwise would
be delivered to downstream waters. Nutrients are necessary to
support aquatic life, but excess nutrients create conditions leading
to eutrophication and hypoxia, in which oxygen concentrations fall
below the level necessary to sustain most within and near-bed animal
life. Thus, the role of streams in influencing nutrient loads can
have significant repercussions for hypoxic areas in downstream
waters.
    f. Headwaters provide critical habitat during one or more life
cycle stages of many organisms capable of moving throughout river
networks. This review found strong evidence that headwaters provide
habitat for complex life-cycle completion, refuge from predators or
adverse physical conditions in rivers, and reservoirs of genetic-
and species-level diversity. Use of headwater streams as habitat is
especially obvious for the many species that migrate between small
streams and marine environments during their life cycles (e.g.,
Pacific and Atlantic salmon, American eels, certain lamprey
species), and the presence of these species within river networks
provides robust evidence of biological connections between
headwaters and larger rivers. In prairie streams, many fishes swim
upstream into tributaries to release eggs, which develop as they are
transported downstream. Small streams also provide refuge habitat
for riverine organisms seeking protection from temperature extremes,
flow extremes, low dissolved oxygen, high sediment levels, or the
presence of predators, parasites, and competitors.

B. Riparian/Floodplain Waters

    Wetlands and open waters in landscape settings that have
bidirectional hydrologic exchanges with streams or rivers (e.g.,
wetlands and open waters in riparian areas and floodplains) are
chemically, physically, or biologically connected with rivers via
the export of channel-forming sediment and woody debris, temporary
storage of local groundwater that supports baseflow in rivers, and
transport of stored organic matter. They remove and transform excess
nutrients such as nitrogen and phosphorus. They provide nursery
habitat for breeding fish, colonization opportunities for stream
invertebrates, and maturation habitat for stream insects. Moreover,
wetlands in this landscape setting serve an important role in the
integrity of downstream waters because they also act as sinks by
retaining floodwaters, sediment, nutrients, and contaminants that
could otherwise negatively impact the condition or function of
downstream waters.
    Key Findings:
    a. Riparian areas act as buffers that are among the most
effective tools for mitigating nonpoint source pollution. The
wetland literature shows that collectively, riparian wetlands
improve water quality through assimilation, transformation, or
sequestration of nutrients, sediment and other pollutants--such as
pesticides and metals--that can affect downstream water quality.
These pollutants enter wetlands via various pathways that include
various sources such as dry and wet atmospheric deposition, some
runoff from upland agricultural and urban areas, spray drift, and
subsurface water flows, as well as point sources such as outfalls,
pipes, and ditches.
    b. Riparian and floodplain areas connect upland and aquatic
environments through both surface and subsurface hydrologic flow
paths. These areas are therefore uniquely situated in watersheds to
receive and process

waters that pass over densely vegetated areas and through subsurface
zones before reaching streams and rivers. When contaminants reach a
riparian or floodplain area, such materials can be sequestered in
sediments, assimilated into the wetland plants and animals,
transformed into less harmful forms or compounds, or lost to the
atmosphere. Wetland potential for biogeochemical transformations
(e.g., denitrification) that can improve the quality of water
entering streams and rivers is influenced by factors present in
riparian areas and floodplains, including anoxic conditions, shallow
water tables, slow organic matter decomposition, wetland plant
communities, permeable soils, and complex topography.
    c. Riparian and floodplain areas can reduce flood peaks by
storing and desynchronizing floodwaters. They also can contribute to
maintenance of flow by recharging alluvial aquifers. Many studies
have documented the ability of riparian and floodplain areas to
reduce flood pulses by storing excess water from streams and rivers.
One review of wetland studies reported that riparian wetlands
reduced or delayed floods in 23 of 28 studies. For example, peak
discharges between upstream and downstream gauging stations on the
Cache River in Arkansas were reduced 10-20% primarily due to
floodplain water storage.
    d. Riparian and floodplain areas store large amounts of sediment
and organic matter from upland areas before those sediments enter
the stream. For example, riparian areas have been shown to filter
80-90% of sediments leaving agricultural fields in North Carolina.
(A. Cooper, et al., ``Riparian Areas as Filters for Agricultural
Sediment,'' Soil Science Society of America Proceedings 51:416-420
(1987); R.B. Daniels, and J.G. Gilliam, ``Sediment and Chemical Load
Reduction by Grass and Riparian Filters,'' Soil Science Society of
America Journal 60:246-251 (1996); R.J. Naiman, and H. Decamps,
``The Ecology of Interfaces: Riparian Zones,'' Annual Review of
Ecology and Systematics 28:621-658 (1997)).
    e. Ecosystem function within a river system is driven by
interactions between the physical environment and the diverse
biological communities living within the river system. Movements of
organisms connect aquatic habitats and populations in different
locations through several processes important for the survival of
individuals, populations, and species, and for the functioning of
the river ecosystem. For example, lateral expansion and contraction
of the river in its floodplain results in an exchange of matter and
organisms, including fish populations that are adapted to use
floodplain habitat for feeding and spawning during high water.
Refuge populations of aquatic plants in floodplains can become
important seed sources for the river network, especially if
catastrophic flooding scours vegetation and seed banks in other
parts of the channel. Many invertebrates exploit temporary
hydrologic connections between rivers and floodplain wetland
habitats, moving into these wetlands to feed, reproduce, or avoid
harsh environmental conditions and then returning to the river
network. Amphibians and aquatic reptiles in many parts of the
country commonly use both streams and wetlands, including wetlands
in riparian and floodplain areas, to hunt, forage, overwinter, rest,
or hide from predators.

C. Unidirectional Wetlands

    Wetlands and open waters in landscape settings that lack
bidirectional hydrologic exchanges with downstream waters (e.g.,
many prairie potholes, vernal pools, and playa lakes) provide
numerous functions that can benefit downstream water quality and
integrity. These functions include storage of floodwater; retention
and transformation of nutrients, metals, and pesticides; and re-
charge of groundwater sources of river baseflow. The functions and
effects of this diverse group of wetlands, hereafter referred to as
``unidirectional wetlands,'' clearly affect the condition of
downstream waters if there is a surface or shallow subsurface water
connection to the river network. In unidirectional wetlands that are
not connected to the river network through surface or shallow
subsurface water, the type and degree of connectivity varies
geographically within a watershed and over time. Because such
wetlands occur on a gradient of connectivity, it is difficult to
generalize about their effects on downstream waters. This evaluation
is further complicated because, for certain functions (e.g.,
sediment removal and water storage), downstream effects arise from
wetland isolation, rather than connectivity. The literature reviewed
does not provide sufficient information to evaluate or generalize
about the degree of connectivity (absolute or relative) or the
downstream effects of wetlands in unidirectional landscape settings.
However, evaluations of connectivity of individual wetlands or
groups of wetlands could be possible through case-by-case analysis.
Further, while the review did not specifically address other
unidirectional water bodies, the conclusions apply to these water
bodies (e.g., ponds and lakes that lack surface water inlets) as
well, since the same principals govern hydrologic connectivity
between these water bodies and downstream waters.
    Key Findings:
    a. Water storage by wetlands well outside of riparian or
floodplain areas can affect streamflow. Hydrologic models of prairie
potholes in the Starkweather Coulee subbasin (North Dakota) that
drain to Devils Lake indicate that increasing the volume of pothole
storage across the sub-basin by approximately 60% caused simulated
total annual streamflow to decrease 50% during a series of dry years
and 20% during wet years. Similar simulation studies of watersheds
that feed the Red River of the North in North Dakota and Minnesota
demonstrated qualitatively comparable results, suggesting that the
ability of potholes to modulate streamflow may be widespread across
portions of the prairie pothole region. This work also indicates
that reducing wetland water storage capacity by connecting formerly
isolated potholes through ditching or drainage to the Devils Lake
and Red River basins could increase stormflow and contribute to
downstream flooding. In many agricultural areas already crisscrossed
by extensive drainage systems, total streamflow and baseflow are
enhanced by directly connecting potholes to stream networks. The
impacts of changing streamflow are numerous, including altered flow
regime, stream geomorphology, habitat, and ecology. The presence or
absence of an effect of prairie pothole water storage on streamflow
depends on many factors, including patterns of precipitation,
topography and degree of human alteration. For example, in parts of
the prairie pothole region with low precipitation, low stream
density, and little human alteration, hydrologic connectivity
between prairie potholes and streams or rivers is likely to be low.
    b. Unidirectional wetlands act as sinks and transformers for
various pollutants, especially nutrients, which pose a serious
pollution problem in the United States. In one study, sewage
wastewaters were applied to forested unidirectional wetlands in
Florida for a period of 4.5 years. More than 95% of the phosphorus,
nitrate, ammonium, and total nitrogen were removed by the wetland
during the study period, and 66-86% of the nitrate removed was
attributed to the process of denitrification. In another study,
sizeable phosphorus retention occurred in unidirectional marshes
that comprised only 7% of the lower Lake Okeechobee basin area in
Florida. A unidirectional bog in Massachusetts was reported to
sequester nearly 80% of nitrogen inputs from various sources,
including atmospheric deposition, and prairie pothole wetlands in
the upper Midwest were found to remove >80% of the nitrate load via
denitrification. A large unidirectional prairie marsh was found to
remove 86% of nitrate, 78% of ammonium, and 20% of phosphate through
assimilation and sedimentation, sorption, and other mechanisms.
Together, these and other studies indicate that on-site removal of
nutrients by unidirectional wetlands is significant and
geographically widespread. The effects of this removal on rivers are
generally not reported in the literature.
    c. Biological connectivity can occur between unidirectional
wetlands and downstream waters through movement of amphibians,
aquatic seeds, macroinvertebrates, reptiles, and mammals. Many
species in those groups that use both stream and wetland habitats
are capable of dispersal distances equal to or greater than
distances between many unidirectional wetlands and river networks.
Unidirectional wetlands can be hydrologically connected directly to
river networks through channels, non-channelized surface flow, or
subsurface flows. A wetland surrounded by uplands is defined as
``geographically isolated.'' Our review found that in some cases,
wetland types such as vernal pools and coastal depressional wetlands
are collectively, and incorrectly, referred to as geographically
isolated. Technically, the term ``geographically isolated'' should
be applied only to the particular wetlands within a type or class
that are completely surrounded by uplands. Furthermore, ``geographic
isolation'' should not be confused with functional isolation,
because geographically isolated wetlands can still have hydrological
and biological connections to downstream waters.

    d. Unidirectional wetlands occur along a gradient of hydrologic
connectivity-isolation with respect to river networks, lakes, or
marine/estuarine water bodies. This gradient includes, for example,
wetlands that serve as origins for stream channels that have
permanent surface water connections to the river network; wetlands
with outlets to stream channels that discharge to deep groundwater
aquifers; geographically isolated wetlands that have local
groundwater or occasional surface water connections to downstream
waters; and geographically isolated wetlands that have minimal
hydrologic connection to other water bodies (but which could include
surface and subsurface connections to other wetlands). The existence
of this gradient among wetlands of the same type or in the same
geographic region can make it difficult to determine or generalize,
from the literature alone, the degree to which particular wetlands
(individually or as classes), including geographically isolated
wetlands, are hydrologically connected.
    e. A related issue is that spatial scale must be considered when
determining geographic isolation. Individual wetlands that are
geographically isolated could be connected to downstream waters when
considered as a complex (a group of interacting wetlands). This
principle was demonstrated in a recent study that examined a
depressional wetland complex on the Texas coastal plain. These
wetlands have been considered as a type of geographically isolated
wetlands. Collectively, however, they are geographically and
hydrologically connected to downstream waters in the area. During an
almost 4-year study period, nearly 20% of the precipitation that
fell on the wetland complex flowed as surface runoff through an
intermittent stream to a nearby waterway, the Armand Bayou. Thus,
wetland complexes could have connections to downstream waters
through stream channels even when the individual wetland components
are geographically isolated.

3. Closing Comments

    The strong hydrologic connectivity of river networks is apparent
in the existence of stream channels that form the physical structure
of the network itself. Given the discussion above, it is clear that
streams and rivers are much more than a system of physical channels
for conveying water and other materials downstream, but the presence
of physical channels is one strong line of evidence for surface
water connections from tributaries, or water bodies of other types,
to downstream waters. Physical channels are defined by continuous
bed and bank structures, which may include apparent disruptions
(such as by bedrock outcrops, braided channels, flow-through
wetlands) associated with changes in the material and gradient over
and through which water flows. The continuation of bed and banks
down gradient from such disruptions is evidence of the surface
connection with the channel that is up gradient of the perceived
disruption.
    The structure and function of rivers are highly dependent on the
constituent materials that are stored in and transported through
them. Most of these materials, broadly defined here as any chemical,
physical, or biological entity, including, but not limited to,
water, heat energy, sediment, wood, organic matter, nutrients,
chemical contaminants, and organisms, originate outside of the
river: They originate from either the upstream river network or
other components of the river system, and then are transported to
the river by water movement or other mechanisms. Thus, the
fundamental way in which streams and wetlands affect river structure
and function is by altering fluxes of materials to the river. The
control of material fluxes depends on two key factors: (1) Functions
within streams and wetlands that affect material fluxes, and (2)
connectivity (or isolation) between streams and wetlands and rivers
that allows (or prevents) transport of materials between the
systems.
    Absence of channels does not, however, mean that a wetland or
open water is isolated or only infrequently connected to downstream
waters. Areas that are infrequently flooded by surface water can be
connected more regularly through shallow groundwater or through
dispersal among biological populations and communities. Such
wetlands and open waters also can reduce flood peaks by storing
flood waters, filter large amounts of sediment and nutrients from
upland areas, influence stream geomorphology by providing woody
debris and sediment, and regulate stream temperature. They also
serve as sources of food for river biota and sources of genetic
diversity for populations of stream invertebrates.
    Unidirectional wetlands can reduce and attenuate floods through
water storage, and can recharge groundwater, thereby contributing to
stream and river baseflow. These wetlands also affect nutrient
delivery and improve water quality by functioning as sources of food
and as sinks for metals, pesticides, excess nutrients. Biological
connectivity can also occur between unidirectional wetlands and
downstream waters, through movement of amphibians, aquatic insects,
aquatic reptiles, migratory birds, and riverine mammals that require
or opportunistically use both river and wetland or open water
habitats. However, given a geographically isolated wetland for which
a surface water connection cannot be observed, it is difficult to
assess its degree of connectivity with the river network without
site-specific data.
    Additionally, caution should be used in interpreting
connectivity for wetlands based on their being designated as
``geographically isolated'' since (a) the term can be mistakenly
applied to a heterogeneous group of wetlands that can include
wetlands that are not geographically isolated, (b) wetlands with
permanent channels could be miscategorized as geographically
isolated if the designation is based on maps or imagery with
inadequate spatial resolution, obscured views, etc., and (c) wetland
complexes could have connections to downstream waters through stream
channels even if individual wetlands within the complex are
geographically isolated. Thus, the term ``geographically isolated''
should only be applied to groups of wetlands if they fit the
technical definition (i.e., they are surrounded by uplands).
Further, even geographically isolated wetlands can be connected to
other wetlands and downstream waters through groundwater
connections, occasional spillage, or biological connections. Thus,
the term ``geographically isolated'' should not be used to infer
lack of hydrologic, chemical, or biological connectivity.
    Lastly, to understand the health, behavior, and sustainability
of downstream waters, effects of small water bodies in a watershed
need to be considered in aggregate. The contribution of material by
a particular stream and wetland might be small, but the aggregate
contribution by an entire class of streams and wetlands (e.g., all
ephemeral streams in the river network) might be substantial. For
example, western vernal pools typically occur within ``vernal pool
landscapes'' or complexes of pools in which swales connect pools to
each other and to seasonal streams, and in which the hydrology and
ecology are tightly coupled with the local and regional geological
processes that formed them. The vernal pool basins, swales, and
seasonal streams are part of a single surface water and shallow
groundwater system connected to the river network when seasonal
precipitation exceeds storage capacity of the wetlands. Since rivers
develop and respond over time and are functions of the whole
watershed, understanding the integration of contributions and
effects over time is also necessary to have an accurate
understanding of the system, taking into account the duration and
frequency of material export and delivery to downstream waters. In
addition, when considering the effect of an individual stream or
wetland, it is important to include the cumulative effect of all
materials that originate from it, rather than each material
individually, to understand that water body's influence on
downstream waters.

Part II: Additional Scientific Support

i. Tributaries

    The agencies propose that all waters that meet the proposed
definition of tributary are ``waters of the United States'' because
they meet Justice Kennedy's test for jurisdiction under Rapanos. In
other words, the agencies are asserting that all tributaries have a
significant nexus with traditional navigable waters, interstate
waters, and/or the territorial seas. EPA and the Corps' longstanding
definition of ``waters of the United States'' has included
tributaries. That regulation was based on the agencies' historic
view of the scope of the CWA and the general scientific
understanding about the ecological and hydrological relationship
between waters.
    Tributaries have a substantial impact on the chemical, physical,
or biological integrity of waters into which they eventually flow--
including traditional navigable waters, interstate waters, and the
territorial seas. The great majority of tributaries are headwater
streams, and whether they are perennial, intermittent, or ephemeral,
they play an important role in the transport of water, sediments,
organic matter, pollutants, nutrients, and organisms to downstream
environments. Tributaries serve to store

water (thereby reducing flooding), provide biogeochemical functions
that help maintain water quality, trap and transport sediments,
transport, store and modify pollutants, provide habitat for plants
and animals, and sustain the biological productivity of downstream
rivers, lakes and estuaries. These conclusions are strongly
supported in the scientific literature, as discussed below.
    Headwater streams are the smallest channels where stream flows
begin, and often occur at the outer rims of a watershed. Typically
these are first-order streams (i.e., they do not have any other
streams flowing into them). However, headwater streams can include
streams with multiple tributaries flowing into them and can be
perennial, intermittent or ephemeral, but are still located near the
channel origins of the tributary system in a watershed.
    Protection of tributaries under the CWA is critically important
because they serve many important functions which directly influence
the integrity of downstream waters. It is necessary to regulate the
entire tributary system to fulfill the objective of the CWA, because
discharges of pollutants into the tributary system adversely affect
the chemical, physical, or biological integrity of these waters. For
example, destruction or modification of headwater streams has been
shown to affect the integrity of downstream waters, in part through
changes in hydrology, chemistry and stream biota. M.C. Freeman, et
al., ``Hydrologic Connectivity and the Contribution of Stream
Headwaters to Ecological Integrity at Regional Scales,'' Journal of
the American Water Resources Association 43:5-14. (2007); M.S.
Wipfli., et al., ``Ecological Linkages between Headwaters and
Downstream Ecosystems: Transport of Organic Matter, Invertebrates,
and Wood Down Headwater Channels,'' Journal of the American Water
Resources Association 43:72-85 (2007). Additionally, activities such
as discharging a pollutant into one part of the tributary system are
well-documented to affect, at times, other parts of the system, even
when the point of discharge is far upstream from the navigable water
that experiences the effect of the discharge. In order to protect
traditional navigable waters, interstate waters, and the territorial
seas it is also critically important to protect tributaries as
defined in today's proposal that are upstream from those waters.

A. The Agencies Have Concluded That Tributaries, as Defined in the
Proposed Rule, Have a Significant Nexus

    The scientific literature documents that tributary streams,
including perennial, intermittent, and ephemeral streams, and
certain categories of ditches are integral parts of river networks
because they are directly connected to rivers via permanent surface
features (channels and associated alluvial deposits) that
concentrate, mix, transform, and transport water and other
materials, including food resources, downstream. Tributaries
transport, and often transform, chemical elements and compounds,
such as nutrients, ions, dissolved and particulate organic matter
and contaminants, influencing water quality, sediment deposition,
nutrient availability, and biotic functions in rivers. Streams also
are biologically connected to downstream waters by dispersal and
migration, processes which have critical implications for aquatic
populations of organisms that use both headwater and river or open
water habitats to complete their life cycles or maintain viable
populations. The scientific literature clearly demonstrates that
cumulatively, streams exert strong influence on the character and
functioning of rivers. In light of these well documented connections
and functions, the agencies concluded that tributaries, as defined,
alone or in combination with other tributaries in a watershed,
significantly affect the chemical, physical, or biological integrity
of a traditional navigable water, interstate water, or the
territorial seas. The scientific literature supports this conclusion
for ephemeral tributaries, as well as for intermittent and perennial
tributaries; for tributaries both near to and far from the
downstream traditional navigable water, interstate water, or the
territorial seas; and for natural tributaries or man-altered
tributaries, which may include certain ditches and canals.
    The discussion below summarizes the key points in the literature
regarding the chemical, physical, and biological connections and
functions of tributaries that significantly affect downstream
waters. In addition, the evidence regarding headwater streams and
non-perennial streams, types of tributaries whose important
functional relationships to downstream traditional navigable waters
and interstate waters might not be obvious, is summarized. The
scientific literature does not use legal terms like ``traditional
navigable water,'' ``interstate water,'' or ``the territorial
seas.'' Rather, the literature assesses tributaries in terms of
their connections to and effects on downstream waters in a
watershed. While the agencies define as ``waters of the United
States'' tributaries only in watersheds which drain to a traditional
navigable water, interstate water, or the territorial seas, that
distinction does not affect the conclusions of the scientific
literature with respect to the effects of tributaries on downstream
waters.

B. Tributaries Significantly Affect the Physical Integrity of (a)(1)
Through (a)(3) Waters

    Tributaries, even when seasonally dry, are the dominant source
of water in most rivers, rather than direct precipitation or
groundwater input to main stem river segments. See, e.g., Report at
4-3 (citing T.C. Winter, 2007, ``The role of groundwater in
generating streamflow in headwater areas and in maintaining base
flow,'' Journal of the American Water Resources Association 43:15-
25; P.A. Bukaveckas, ``Rivers,'' in G.E. Likens, ed., Encyclopedia
of Inland Waters, Vol. 1 (Elsevier: Oxford, 2009)). Distant
headwaters with stronger connections to groundwater or consistently
higher precipitation levels than downstream reaches contribute more
water to downstream rivers. In the northeastern United States
headwater streams contribute greater than 60% of the water volume in
larger tributaries, including navigable rivers. See, e.g., id.
(citing R.B. Alexander, et. al., ``The role of headwater streams in
downstream water quality,'' Journal of the American Water Resources
Association 43:41-59 (2007)). The contributions of tributaries to
river flows are often readily measured or observed, especially
immediately below confluences, where tributary flows increase the
flow volume and alter physical conditions, such as water
temperature, in the main stream. The physical effects of tributaries
are particularly clear after intense rainfall occurs over only the
upper tributary reaches of a river network. For example, a study of
ephemeral tributaries to the Rio Grande in New Mexico found that
after a storm event contributions of the stormflow from ephemeral
tributaries accounted for 76% of the flow of the Rio Grande. See,
e.g., id. at 4-5 (citing E.R. Vivoni, et. al., ``Analysis of a
Monsoon Flood Event in an Ephemeral Tributary and Its Downstream
Hydrologic Effects,'' Water Resources Research 42:W03404 (2006)). A
key effect of tributaries on the hydrologic response of river
networks to storm events is dispersion, or the spreading of water
output from a drainage basin over time. Hydrologic dispersion of
connected tributaries influence the timing and volume of water
reaching a river network outlet. See, e.g., id. at 4-5 to 4-6
(citing P. M. Saco and P. Kumar, ``Kinematic dispersion in stream
networks coupling hydraulics and network geometry,'' Water Resources
Research 38:1244 (2002)). Tributaries also can reduce the amount of
water that reaches downstream rivers and minimize downstream
flooding, often through infiltration or seepage through channel beds
and banks or through evapotranspiration. See, e.g., id. at 4-8
(citing S.K. Hamilton, et al., ``Persistence of Aquatic Refugia
between Flow Pulses in a Dryland River System (Cooper Creek,
Australia),'' Limnology and Oceanography 50:743-754 (2005); J.F.
Costelloe, et.al., ``Determining Loss Characteristics of Arid Zone
River Waterbodies,'' River Research and Applications 23:715-731
(2007)).
    One of the primary functions of tributaries is transporting
sediment to downstream waters. Tributaries, particularly headwaters,
shape and maintain river channels by accumulating and gradually or
episodically releasing sediment and large woody debris into river
channels. Sediment transport is also clearly provided by ephemeral
streams. Effects of the releases of sediment and large woody debris
are especially evident at tributary-river confluences, where
discontinuities in flow regime and temperature clearly demonstrate
physical alteration of river structure and function by headwater
streams. Report at 4-10, 4-14. Sediment movement is critical for
maintaining the river network, including rivers that are considered
to be traditional navigable waters, as fluvial (produced by the
action of a river or stream) sediments are eroded from some channel
segments, and deposited in others downstream to form channel
features, stream and riparian habitat which supports the biological
communities resident downstream, and influence the river
hydrodynamics. See, e.g., J.L. Florsheim, et al., ``Bank Erosion as
a Desirable Attribute of Rivers,'' Bioscience 58:519-29 (2008);
Report at 4-9 (citing M. Church, ``Bed material transport and the
morphology of alluvial river channels,'' Annual Review of Earth and

Planetary Sciences: 325-354 (2006)). While essential to river
systems, too much sediment can impair ecological integrity by
filling interstitial spaces, blocking sunlight transmission through
the water column, and increasing contaminant and nutrient
concentrations. Report at 4-9 (citing P.J. Wood and P.D. Armitage,
``Biological Effects of Fine Sediment in the Lotic Environment,''
Environmental Management 21:203-217 (1997)). Over sedimentation thus
can reduce photosynthesis and primary productivity within the stream
network and otherwise have harmful effects on downstream biota,
including on the health and abundance of fish, aquatic macrophytes
(plants), and aquatic macroinvertebrates that inhabit downstream
waters. See, e.g., Wood and Armitage 1997. Headwater streams tend to
trap and store sediments behind large structures, such as boulders
and trees, that are transported downstream only during infrequent
large storm events. See Report at 4-10, 4-12 (citing L.E. Benda, and
T.W. Cundy, ``Predicting deposition of debris flows in mountain
channels,'' Canadian Geotechnical Journal 27:409-417 (1990); T. Gomi
and R.C. Sidle, ``Bed load transport in managed steep-gradient
headwater streams of southeastern Alaska,'' Water Resources Research
39:1336 (2003); L.E. Benda, et al., ``Geomorphology of steepland
headwaters: The transition from hillslopes to channels,'' Journal of
the American Water Resources Association 41:835-851 (2005); P.E.
Bigelow, et al., ``On Debris Flows, River networks, and the Spatial
Structure of Channel Morphology,'' Forest Science 53:220-238 (2007);
J.P.R. Gooderham, et al., ``Upstream Heterogeneous Zones: Small
Stream Systems Structured by a Lack of Competence?'' Journal of the
North American Benthological Society 26:365-374 (2007)).
    Tributaries can greatly influence water temperatures in
tributary networks. This is important because water temperature is a
critical factor governing the distribution and growth of aquatic
life, both directly (through its effects on organisms) and
indirectly (through its effects on other physiochemical properties,
such as dissolved oxygen and suspended solids). Id. at 4-13 (citing
J.D. Allan, Stream Ecology--Structure and Function of Running Waters
(New York, NY: Chapman & Hall, 1995)). For instance, water
temperature controls metabolism and level of activity in cold-
blooded species like fish, amphibians, and aquatic invertebrates.
See, e.g., G.G. Ice, ``Chapter 3: Stream Temperature and Dissolved
Oxygen,'' in J.D. Stednick, ed., Hydrologic and Biological Responses
to Forest Practices (Springer, 2008). Temperature can also control
the amount of dissolved oxygen in streams, as colder water holds
more dissolved oxygen, which fish and other fauna need to breathe.
Connections between tributaries and downstream rivers can affect
water temperature in river networks. See, e.g., Report at 4-13
(citing S. Knispel, and E. Castella, ``Disruption of a Longitudinal
Pattern in Environmental Factors and Benthic Fauna by a Glacial
Tributary,'' Freshwater Biology 48:604-618 (2003); S.P. Rice, et
al., ``The Ecological Importance of Tributaries and Confluences,''
in S.P. Rice, et al., ed., River Confluences, Tributaries and the
Fluvial Network, (Chichester, UK: John Wiley & Sons, 2008), pp. 209-
242)). In particular, tributaries provide both cold and warm water
refuge habitats that are critical for protecting aquatic life. Id.
at 4-32. Because headwater tributaries often depend on groundwater
inputs, temperatures in these systems tend to be warmer in the
winter (when groundwater is warmer than ambient temperatures) and
colder in the summer (when groundwater is colder than ambient
temperatures) relative to downstream waters. Id. (citing G. Power,
et al., ``Groundwater and Fish: Insights from Northern North
America,'' Hydrological Processes 13:401-422 (1999)). Thus
tributaries provide organisms with both warm water and coldwater
refuges at different times of the year. Id. (citing R.A. Curry, et
al., ``Use of Small Streams by Young Brook Trout Spawned in a
Lake,'' Transactions of the American Fisheries Society 126:77-83
(1997); C.V. Baxter, and F.R. Hauer, ``Geomorphology, Hyporheic
Exchange and Selection of Spawning Habitat by Bull Trout (Salvelinus
confluentus),'' Canadian Journal of Fisheries and Aquatic Sciences
57: 1470-1481 (2000); T.R. Labbe, and K.D. Fausch, ``Dynamics of
Intermittent Stream Habitat Regulate Persistence of a Threatened
Fish at Multiple Scales,'' Ecological Applications 10:1774-1791
(2000); M.J. Bradford, et al., ``Ecology of Juvenile Chinook Salmon
in a Small Non-natal Stream of the Yukon River Drainage and the Role
of Ice Conditions on Their Distribution and Survival,'' Canadian
Journal of Zoology-Revue Canadienne De Zoologie 79:2043-2054
(2001)). For example, when temperature conditions in downstream
waters are adverse, fish can travel upstream and use tributaries as
refuge habitat. Id. (citing Curry et al. 1997; M.A. Cairns, et al.,
``Influence of Summer Stream Temperatures on Black Spot Infestation
of Juvenile Coho Salmon in the Oregon Coast Range,'' Transactions of
the American Fisheries Society 134:1471-1479 (2005)). Tributaries
also help buffer temperatures in downstream waters. Id. at 4-13 to
4-14 (citing D. Caissie, ``The thermal regime of rivers: A review,''
Freshwater Biology 51:1389-1406 (2006). Temperatures in tributaries
affect downstream water temperature many kilometers away. Id. at 4-
14 (citing B. Gardner, and P.J. Sullivan, ``Spatial and Temporal
Stream Temperature Prediction: Modeling Nonstationary Temporal
Covariance Structures,'' Water Resources Research 40:W01102 doi
(2004); B.R. Johnson, et al., ``Use of Spatially Explicit
Physicochemical Data to Measure Downstream Impacts of Headwater
Stream Disturbance,'' Water Resources Research 46:W09526 (2010)).

C. Tributaries Significantly Affect the Chemical Integrity of (a)(1)
Through (a)(3) Waters

    Tributaries transform and export significant amounts of
nutrients and carbon to downstream waters, serving important source
functions that greatly influence the chemical integrity of
downstream waters. Organic carbon, in both dissolved and particulate
forms, exported from tributaries is consumed by downstream
organisms. The organic carbon that is exported downstream thus
supports biological activity (including metabolism) throughout the
river network. See, e.g., Report at 4-22 (citing S.G. Fisher and
G.E. Likens, ``Energy Flow in Bear Brook, New Hampshire: An
Integrative Approach to Stream Ecosystem Metabolism,'' Ecological
Monographs 43: 421-439 (1973); J.L. Meyer, ``The Microbial Loop in
Flowing Waters,'' Microbial Ecology 28:195-199 (1994); J.B. Wallace,
et al. ``Multiple Trophic Levels of a Forest Stream Linked to
Terrestrial Litter Inputs,'' Science 277:102-104 (1997); R.O. Hall
and J.L. Meyer, ``The Trophic Significance of Bacteria in a
Detritus-Based Stream Food Web,'' Ecology 79:1995-2012 (1998); R.O.
Hall, et al., ``Organic Matter Flow in Stream Food Webs with Reduced
Detrital Resource Base,'' Ecology 81:3445-3463 (2000); C.
Augspurger, et al., ``Tracking Carbon Flow in a 2-Week-Old and 6-
Week-Old Stream Biofilm Food Web,'' Limnology and Oceanography
53:642-650 (2008)). Much or most of the organic carbon that is
exported from tributaries has been altered either physically or
chemically by ecosystem processes within the tributary streams,
particularly by headwater streams.
    Nutrient export from tributaries has a large effect on
downstream water quality, as excess nutrients from surface runoff
from lawns and agricultural fields can cause algal blooms that
reduce dissolved oxygen levels and increase turbidity in rivers,
lakes, estuaries, and territorial seas. Water low in dissolved
oxygen cannot support aquatic life; it is widely-recognized that
this phenomenon has resulted in the devastation of commercial and
recreational fisheries in the northern Gulf of Mexico. Committee on
Environment and Natural Resources, Integrated Assessment of Hypoxia
in the Northern Gulf of Mexico (Washington, DC: National Science and
Technology Council, 2000). The amount of nitrogen that is exported
downstream varies depending on stream size, and how much nitrogen is
present in the system. Nitrogen loss is greater in smaller, shallow
streams, most likely because denitrification and settling of
nitrogen particles occur at slower rates in deeper channels. Report
at 4-16 (citing R.G. Alexander, et al., ``Effect of Stream Channel
Size on the Delivery of Nitrogen to the Gulf of Mexico,'' Nature
403:758-761 (2000)). At low loading rates, the biotic removal of
dissolved nitrogen from water is high and occurs primarily in small
tributaries, reducing the loading to larger tributaries and rivers
downstream. At high nitrogen loading rates, tributaries become
nitrogen saturated and are not effectively able to remove nitrogen,
resulting in high nitrogen export to rivers. Id. at 4-18 (citing
P.J. Mulholland, et al., ``Stream Denitrification across Biomes and
Its Response to Anthropogenic Nitrate Loading,'' Nature 452:202-205
(2008)). The transport of nitrogen and phosphorus downstream has
also been well-documented, particularly in the cases of the Gulf of
Mexico and the Chesapeake Bay. Tributary streams in the uppermost
portions of the Gulf and Bay watersheds transport the majority of
nutrients to the downstream waters; an estimated 85% of nitrogen
arriving at the hypoxic zone in the Gulf originates in the

upper Mississippi (north of Cairo, Illinois) and the Ohio River
Basins. D. Goolsby, et al., Topic Report 3, Flux and Sources of
Nutrients in the Mississippi-Atchafalaya River Basin (Washington,
DC: National Science and Technology Council Committee on Environment
and Natural Resources, 1999). The export of nutrients from streams
in the Mississippi River Basin has an effect on anoxia, or low
oxygen levels, in the Gulf. Report at 4-17 (citing N.N. Rabalais, et
al., ``Gulf of Mexico Hypoxia, a.k.a. `the Dead Zone,' '' Annual
Review of Ecology and Systematics 33:235-263 (2002)). Similarly,
nutrient loads from virtually the entire 64,000 square mile
watershed affect water quality in the Chesapeake Bay. Simulation
tools have been used to determine the nutrient and sediment load
reductions that must be made at many different points throughout the
entire watershed in order to achieve acceptable water quality in the
mainstem of the Bay. These reductions included specific annual
nitrogen caps on the upper reaches of the Susquehanna River in New
York State, more than 400 miles from the mouth of the Chesapeake
Bay. See e.g., U.S. Environmental Protection Agency (EPA), Region
III, Chesapeake Bay Program Office, Setting and Allocating the
Chesapeake Bay Basin Nutrient and Sediment Loads: The Collaborative
Process, Technical Tools and Innovative Approaches, EPA 903-R-03-007
(Washington, DC: EPA, 2003); Rabalais et al. 2002.
    Although tributaries export nutrients, carbon, and contaminants
downstream, they also transform these substances. Phosphorous and
nitrogen arrive at downstream waters having already been cycled, or
taken up and transformed by living organisms, many times in
headwater and smaller tributaries. Report at 4-19 to 4-20, 6-3 to 6-
4 (citing J.R. Webster, and B.C. Patten, ``Effects of watershed
perturbation on stream potassium and calcium dynamics,'' Ecological
Monographs 49:51-72 (1979); J.D. Newbold, et al., ``Measuring
nutrient spiraling in streams,'' Canadian Journal of Fisheries and
Aquatic Sciences 38:860-863 (1981); J. Elwood, et al., ``Resource
spiraling: An operational paradigm for analyzing lotic ecosystems,''
in T.D. Fontaine and S.M. Bartell, ed., Dynamics of Lotic Ecosystems
(Ann Arbor, MI: Ann Arbor Science, 1983), pp. 3-23; S.H. Ensign, and
M.W. Doyle, ``Nutrient Spiraling in Streams and River Networks,''
Journal of Geophysical Research-Biogeosciences 111:G04009 (2006)).
In addition, some of the nutrient that is taken up as readily
available inorganic forms is released back to the water as organic
forms that are less available for biotic uptake. Id. at 4-20 (citing
P.J. Mulholland, et al., ``Production of Soluble, High Molecular
Weight Phosphorus and Its Subsequent Uptake by Stream Detritus,''
Verhandlungen des Internationalen Verein Limnologie 23:1190-1197
(1988); S.P. Seitzinger, et al., ``Bioavailability of DON from
Natural and Anthropogenic Sources to Estuarine Plankton,'' Limnology
and Oceanography 47:353-366 (2002)). Similarly, nutrient
incorporated into particulates is not entirely regenerated, but
accumulates in longitudinally increasing particulate loads (i.e.
increases moving downstream). Id. at 4-20 (citing J.L Merriam, et
al., ``Characterizing Nitrogen Dynamics, Retention and Transport in
a Tropical Rainforest Stream Using an in situ N-15 Addition,''
Freshwater Biology 47:143-160 (2002); M.R. Whiles, and W.K. Dodds,
``Relationships between Stream Size, Suspended Particles, and
Filter-Feeding Macroinvertebrates in a Great Plains Drainage
Network,'' Journal of Environmental Quality 31:1589-1600 (2002);
R.O. Hall, et al., ``Hydrologic Control of Nitrogen Removal,
Storage, and Export in a Mountain Stream,'' Limnology and
Oceanography 54:2128-2142 (2009)). Headwater streams have seasonal
cycles in the concentrations of phosphorous and nitrogen that are
delivered downstream by accumulating nutrient derived from
temporarily growing streambed biomass. Id. (citing P.J. Mulholland,
and W.R. Hill, ``Seasonal Patterns in Streamwater Nutrient and
Dissolved Organic Carbon Concentrations: Separating Catchment Flow
Path and In-Stream Effects,'' Water Resources Research 33:1297-1306
(1997); P.J. Mulholland, ``The Importance of In-stream Uptake for
Regulating Stream Concentrations and Outputs of N and P from a
Forested Watershed: Evidence from Long-Term Chemistry Records for
Walker Branch Watershed,'' Biogeochemistry 70:403-426 (2004)). Such
variations have been demonstrated to affect downstream productivity.
Id. (citing P.J. Mulholland, et al., ``Longitudinal Patterns of
Nutrient Cycling and Periphyton Characteristics in Streams: a Test
of Upstream-Downstream Linkage,'' Journal of the North American
Benthological Society 14:357-370 (1995)). Nitrification, the
microbial transformation of ammonium to nitrate, affects the form of
downstream nutrient delivery. Nitrification occurs naturally in
undisturbed headwater streams, but increases sharply in response to
ammonium inputs, thereby reducing potential ammonium toxicity from
pollutant inputs. Id. (citing Newbold, et al., ``Phosphorus Dynamics
in a Woodland Stream Ecosystem: a Study of Nutrient Spiraling,''
Ecology 64:1249-1265 (1983); S.C. Chapra, Surface Water Quality
Modeling (McGraw-Hill, 1996); E.S. Bernhardt, et al., ``Whole-system
Estimates of Nitrification and Nitrate Uptake in Streams of the
Hubbard Brook Experimental Forest,'' Ecosystems 5:419-430 (2002)).
Denitrification, the removal of nitrate from streamwater through
transformation to atmospheric nitrogen, is widespread among
headwater streams; research indicates that small, unimpacted
tributaries can reduce up to 40% of downstream nitrogen delivery
through denitrification. Id. at 4-20 to 4-21 (citing P.J.
Mulholland, et al., ``Stream Denitrification across Biomes and Its
Response to Anthropogenic Nitrate Loading,'' Nature 452:202-205
(2008)). Small tributaries also affect the downstream delivery of
nutrients through abiotic processes. Streams can reduce phosphorus
concentrations through sorption (i.e., ``sticking'') to stream
sediments. Id. at 4-21 (citing J.L. Meyer, ``The Role of Sediments
and Bryophytes in Phosphorus Dynamics in a Headwater Stream
Ecosystem,'' Limnology and Oceanography 24:365-375 (1979)). This is
particularly beneficial to downstream chemical integrity where
phosphorus sorbs to contaminants such as metal hydroxide
precipitates. Id. (citing J.A. Simmons, ``Phosphorus Removal by
Sediment in Streams Contaminated with Acid Mine Drainage,'' Water
Air and Soil Pollution 209:123-132 (2010)).
    Tributaries also store significant amounts of nutrients and
carbon, functioning as important sinks (lags) for river networks so
that they do not reach downstream traditional navigable waters,
interstate waters, or the territorial seas. Small tributary streams
in particular often have the greatest effect on downstream water
quality, in terms of storage and reducing inputs to downstream
waters. For instance, uptake and transformation of inorganic
nitrogen often occurs most rapidly in the smallest tributaries. See,
e.g., id. at 4-18 (citing B.J. Peterson, et al., ``Control of
Nitrogen Export from Watersheds by Headwater Streams,'' Science
292:86-90 (2001)). Small tributaries affect the downstream delivery
of nutrients such as phosphorus through abiotic processes; such
streams can reduce phosphorus concentrations by sorption to stream
sediments.
    Tributaries can also serve as a temporary or permanent source or
sink for contaminants, for instance substances like metals, sodium,
and even dead fish carcasses that adversely affect organisms when
occurring at excessive or elevated concentrations to reduce the
amounts that reach downstream traditional navigable waters,
interstate waters, or the territorial seas. The transport of
contaminants to downstream waters can impact water quality
downstream, if they are not stored in tributaries. See, e.g., id. at
4-26 (citing X. Wang, et al., ``Water Quality Changes as a Result of
Coalbed Methane Development in a Rocky Mountain Watershed,'' Journal
of the American Water Resources Association 43:1383-1399 (2007)).
Tributaries can also serve as at least a temporary sink for
contaminants that would otherwise impair downstream water quality.
See, e.g., id. at 133-134 (citing W.L. Graf, Plutonium and the Rio
Grande: Environmental Change and Contamination in the Nuclear Age
(New York: Oxford University Press, 1994)).
    The distances and extent of metal contaminant transport was
shown in separate studies in the upper Arkansas River in Colorado,
and Clark Fork River in Montana, where past mining activities
impacted the headwater tributaries. River bed sediments showed that
metals originating from the mining and smelting areas in the
headwaters were reaching water bodies up to 550 km downstream. Id.
at 4-26 to 4-27 (citing E.V. Axtmann, and S.N. Luoma, ``Large-scale
Distribution of Metal Contamination in the Fine-grained Sediments of
the Clark Fork River, Montana, USA,'' Applied Geochemistry 6:75-88
(1991); B.A. Kimball, et al., ``Effects of Colloids on Metal
Transport in a River Receiving Acid Mine Drainage, Upper Arkansas
River, Colorado, USA,'' Applied Geochemistry 10:285-306 (1995)).
    Military studies of the distribution, transport, and storage of
radionuclides (e.g., plutonium, thorium, uranium) have provided
convincing evidence for distant chemical

connectivity in river networks because the natural occurrence of
radionuclides is extremely rare. From 1942 to 1952, prior to the
full understanding of the risks of radionuclides to human health and
the environment, plutonium dissolved in acid was discharged
untreated into several intermittent headwater streams that flow into
the Rio Grande at the Los Alamos National Laboratory, New Mexico.
Id. at 4-28 (citing W.L. Graf, Plutonium and the Rio Grande:
Environmental Change and Contamination in the Nuclear Age (New York:
Oxford University Press, 1994); S.L. Reneau, et al., ``Geomorphic
Controls on Contaminant Distribution along an Ephemeral Stream,''
Earth Surface Processes and Landforms 29:1209-1223 (2004)). Also
during this time, nuclear weapons testing occurred west of the upper
Rio Grande near Socorro, New Mexico (Trinity blast site) and in
Nevada, where fallout occurred on mountainous areas with thin soils
that are readily transported to headwater streams in the upper Rio
Grande basin. The distribution of plutonium within the Rio Grande
illustrates how headwater streams transport and store contaminated
sediment that has entered the basin through fallout and from direct
discharge. Los Alamos Canyon, while only representing 0.4% of the
drainage area at its confluence with the Rio Grande, had a mean
annual bedload contribution of plutonium almost seven times that of
the mainstem. Id. (citing Graf 1994). Much of the bedload
contribution occurred sporadically during intense storms that were
out of phase with flooding on the upper Rio Grande. Total estimated
contributions of plutonium between the two sources to the Rio Grande
were approximately 90% from fallout to the landscape and 10% from
direct effluent discharge at Los Alamos National Laboratory. Id.
(citing Graf 1994).

C. Tributaries Significantly Affect the Biological Integrity of (a)(1)
Through (a)(3) Waters

    Tributaries are biologically linked to downstream waters through
the movement of living organisms or their reproductive propagules,
such as eggs or seeds. For organisms that drift with water flow,
biological connections depend on hydrological connections. However,
many aquatic organisms are capable of active movement with or
against water flow, and others disperse actively or passively over
land by walking, flying, drifting, or ``hitchhiking.'' All of these
different types of movement form the basis of biological
connectivity between headwater tributaries and downstream waters.
    Headwater tributaries increase the amount and quality of habitat
available to aquatic organisms. Under adverse conditions, small
tributaries provide safe refuge, allowing organisms to persist and
recolonize downstream areas once adverse conditions have abated.
See, e.g., Report at 4-29 (citing J.L. Meyer and J.B. Wallace,
``Lost Linkages and Lotic Ecology: Rediscovering Small Streams,''
Pages 295-317 in M.C. Press, N. J. Huntly, and S. Levin, editors.
Ecology: Achievement and Challenge (Oxford, UK: Blackwell Science,
2001); A. Meyer et al., ``The Effect of Low Flow and Stream Drying
on the Distribution and Relative Abundance of the Alien Amphipod,
Echinogammarus berilloni (Catta, 1878) in a Karstic Stream System
(Westphalia, Germany),'' Crustaceana 77:909-922 (2004); A.D. Huryn
et al., ``Landscape Heterogeneity and the Biodiversity of Arctic
Stream Communities: A Habitat Template Analysis,'' Canadian Journal
of Fisheries and Aquatic Sciences 62:1905-1919 (2005)). Use of
tributaries by salmon and other anadromous fish for spawning is
well-documented, but even non-migratory species can travel great
distances within the river and tributary networks. See, e.g., id. at
4-31 (citing O.T. Gorman, ``Assemblage Organization of Stream
Fishes: The Effects of Rivers on Adventitious Streams,'' American
Naturalist 128(4): 611-616 (1986); A. L. Sheldon, ``Conservation of
Stream Fishes: Patterns of Diversity, Rarity, and Risk,''
Conservation Biology 2:149-156 (1988); N.P. Hitt and P.L.
Angermeier, ``Evidence for Fish Dispersal from Spatial Analysis of
Stream Network Topology,'' Journal of the North American
Benthological Society 27:304-320 (2008)). Tributaries also serve as
an important source of food for biota in downstream rivers.
Tributaries export plankton, vegetation, fish eggs, insects,
invertebrates like worms or crayfish, smaller fish that originate in
upstream tributaries and other food sources that drift downstream to
be consumed by other animals. See, e.g., id. at 4-29 (citing D.J.
Progar and A.R. Modenke, ``Insect Production from Temporary and
Perennially Flowing Headwater Streams in Western Oregon,'' Journal
of Freshwater Ecology 17:391-407 (2002)). For example, many fish
feed on drifting insects, and numerous studies document the
downstream drift of stream invertebrates that then are eaten by fish
in larger rivers. See, e.g., id. at 4-29 to 4-30 (citing S. Nakano
and M. Murakami, ``Reciprocal Subsidies: Dynamic Interdependence
between Terrestrial and Aquatic Food Webs,'' Proceedings of the
National Academy of Sciences USA 98:166-170 (2001); M.S. Wipfli and
D.P. Gregovich, ``Export of Invertebrates and Detritus from Fishless
Headwater Streams in Southeastern Alaska: Implications for
Downstream Salmonid Production,'' Freshwater Biology 47:957-969
(2002)).
    Biological connectivity also allows gene flow, or genetic
connectivity, among tributary and river populations. Gene flow is
needed to maintain genetic diversity in a species, a basic
requirement for that species to be able to adapt to environmental
change. Populations connected by gene flow have a larger breeding
population size, making them less prone to the deleterious effects
of inbreeding and local extinction. Id. at 4-33 (citing R. Lande and
S. Shannon, ``The role of genetic variation in adaptation and
population persistence in a changing environment,'' Evolution
50:434-437 (1996)). Genetic connectivity exists at multiple scales
and can extend beyond one a single river catchment, and for species
capable of long distance movement (such as salmon), reveals complex
interactions among spatially distant populations of aquatic
organisms Id. (citing J.M. Hughes, et al., ``Genes in Streams: Using
DNA to Understand the Movement of Freshwater Fauna and Their
Riverine Habitat,'' Bioscience 59:573-583 (2009); C.D. Anderson,
``Considering spatial and temporal scale in landscape-genetic
studies of gene flow,'' Molecular Ecology 19:3565-3575 (2010)).

D. Headwater Tributaries Significantly Affect the Chemical, Physical,
or Biological Integrity of (a)(1) Through (a)(3) Waters

    As discussed above, the scientific literature supports the
conclusion that tributaries, including headwater streams, have a
significant nexus to downstream waters based on their contribution
to the chemical, physical, or biological integrity of (a)(1) through
(a)(3) waters. Headwater tributaries, the small streams at the
uppermost reaches of the tributary network, are the most abundant
streams in the United States. See, e.g., id. at 4-2 (citing T.L.
Nadeau and M.C. Rains, ``Hydrological connectivity between headwater
streams and downstream waters: How science can inform policy,''
Journal of the American Water Resources Association 43:118-133
(2007)). Collectively, they help shape the chemical, physical, and
biological integrity of downstream waters, and provide many of the
same functions as non-headwater streams. See, e.g., id. at 1-7 to 1-
8, 4-1. For example, headwater streams reduce the amount of sediment
delivered to downstream waters by trapping sediment from water and
runoff. See, e.g., M. Dieterich and N.H. Anderson, ``Dynamics of
Abiotic Parameters, Solute Removal and Sediment Retention in Summer-
Dry Headwater Stream of Western Oregon,'' Hydrobiologia 379: 1-15
(1998). Headwater streams shape river channels by accumulating and
gradually or episodically releasing sediment and large woody debris
into river channels. They are also responsible for most nutrient
cycling and removal, and thus transforming and changing the amount
of nutrients delivered to downstream waters. See, e.g., Report at 4-
18 (citing B.J. Peterson, et al., ``Control of Nitrogen Export from
Watersheds by Headwater Streams,'' Science 292: 86-90 (2001)). A
close connection exists between the water quality of these streams
and the water quality of traditional navigable waters, interstate
waters, and the territorial seas. See, e.g., State of Ohio
Environmental Protection Agency, Nonpoint Source Impacts on Primary
Headwater Streams (Columbus, OH: Ohio Environmental Protection
Agency, 2003). Activities such as discharging a pollutant into one
part of the tributary system are well-documented to affect other
parts of the system, even when the point of discharge is far
upstream from the navigable water that experiences the effect of the
discharge. See, e.g., F.M. Dunnivant and E. Anders, A Basic
Introduction To Pollutant Fate and Transport: An Integrated Approach
With Chemistry, Modeling, Risk Assessment, and Environmental
Legislation (Hoboken, NJ: John Wiley & Sons, Inc., 2006).
    Headwater streams provide unique habitat and protection for
amphibians, fish, and other aquatic or semi-aquatic species living
in and near the stream that may use the downstream waters for other
portions of their life stages. See, e.g., Report at 1-8; J.L. Meyer,
et al., ``The Contribution of Headwater Streams to Biodiversity in
River Networks,'' Journal of the American Water Resources

Association 43(1): 86-103 (2007). They also serve as migratory
corridors for fish. Tributaries can improve or maintain biological
integrity and can control water temperatures in the downstream
waters. See, e.g., Report at 4-14 (citing J.L. Ebersole, et. al.,
``Cold water patches in warm streams: Physicochemical
characteristics and the influence of shading,'' Journal of the
American Water Resources Association 39:355-368 (2003); B. Gardner,
and P.J. Sullivan, ``Spatial and temporal stream temperature
prediction: Modeling nonstationary temporal covariance structures,''
Water Resources Research 40:1-9 (2004); B.R. Johnson, et al., ``Use
of spatially explicit physicochemical data to measure downstream
impacts of headwater stream disturbance,'' Water Resources Research
46:W09526 (2010)). Headwater streams also provide refuge habitat for
riverine organisms seeking protection from temperature extremes,
flow extremes, low dissolved oxygen, high sediment levels, or the
presence of predators, parasites, and competitors. See, e.g., id. at
4-32 (citing J.C. Scrivener, et al., ``Juvenile Chinook salmon
(Oncorhynchus tshawytscha) utilization of Hawks Creek, a small and
nonnatal tributary of the Upper Fraser River,'' Canadian Journal of
Fisheries and Aquatic Sciences 51:1139-1146 (1994); R.A. Curry, et
al., ``Use of small streams by young brook trout spawned in a
lake,'' Transactions of the American Fisheries Society 126:77-83
(1997); A.M. Pires, et al., ``Seasonal changes in fish community
structure of intermittent streams in the middle reaches of the
Guadiana basin, Portugal,'' Journal of Fish Biology 54:235-249
(1999); M.J Bradford, et al., ``Ecology of juvenile Chinook salmon
in a small nonnatal stream of the Yukon River drainage and the role
of ice conditions on their distribution and survival,'' Canadian
Journal of Zoology-Revue Canadienne De Zoologie 79:2043-2054 (2001);
M.A. Cairns, et al., ``Influence of summer stream temperatures on
black spot infestation of juvenile coho salmon in the Oregon Coast
Range,'' Transactions of the American Fisheries Society 134:1471-
1479 (2005); Wigington, P. J., et al., ``Coho salmon dependence on
intermittent streams,'' Frontiers in Ecology and the Environment
4:513-518 (2006)). Headwater streams serve as a source of food
materials such as insects, larvae, and organic matter to nourish the
fish, mammals, amphibians, and other organisms in downstream
streams, rivers, and lakes. See, e.g., id. at 4-22, 4-24 (citing
S.G., Fisher, and G.E. Likens, ``Energy flow in Bear Brook, New
Hampshire: An integrative approach to stream ecosystem metabolism,''
Ecological Monographs 43:421-439 (1973); J.L. Meyer, ``The microbial
loop in flowing waters,'' Microbial Ecology 28:195-199 (1994); J.B.
Wallace, et al., ``Multiple trophic levels of a forest stream linked
to terrestrial litter inputs,'' Science 277:102-104 (1997); R.O.
Hall, and J.L. Meyer, ``The trophic significance of bacteria in a
detritus-based stream food web,'' Ecology 79:1995-2012 (1998); R.O.
Hall, et al., ``Organic matter flow in stream food webs with reduced
detrital resource base,'' Ecology 81:3445-3463 (2000); T. Gomi, et
al., ``Understanding processes and downstream linkages of headwater
systems,'' Bioscience 52:905-916 (2002); C. Augspurger, et al.,
``Tracking carbon flow in a 2-week-old and 6-week-old stream biofilm
food web,'' Limnology and Oceanography 53:642-650 (2008)).
Disruptions in these biological processes affect the ecological
functions of the entire downstream system. See, e.g., L.A. Kaplan,
et al., ``Patterns of Dissolved Organic Carbon in Transport,''
Limnology and Oceanography 25: 1034-1043 (1980); R.L. Vannote, et.
al., ``The River Continuum Concept,'' Canadian Journal of Fisheries
and Aquatic Sciences 37: 130-37 (1980). Headwater streams can help
to maintain base flow in the larger rivers downstream, which is
particularly important in times of drought. See, e.g., Report at 4-
4, 4-66 (citing P.D. Brooks, and M.M. Lemon, ``Spatial variability
in dissolved organic matter and inorganic nitrogen concentrations in
a semiarid stream, San Pedro River, Arizona,'' Journal of
Geophysical Research-Biogeosciences 112:G03S05.D (2007); Tetzlaff,
and C. Soulsby, ``Sources of baseflow in larger catchments--using
tracers to develop a holistic understanding of runoff generation,''
Journal of Hydrology 359:287-302 (2008)). At the same time, the
network of headwater streams can regulate the flow of water into
downstream waters, mitigating low flow and high flow extremes,
reducing local and downstream flooding, and preventing excess
erosion caused by flooding. See, e.g., United States, U.S. EPA and
USDA/ARS Southwest Watershed Research Center, EPA/600/R-08/134, ARS/
2330462008: The Ecological and Hydrological Significance of
Ephemeral and Intermittent Streams in the Arid and Semi-arid
American Southwest (Washington, DC: U.S. EPA and USDA/ARS Southwest
Watershed Research Center, Levick et al., 2008) (Levick et al.
2008).

F. Ephemeral and Intermittent Tributaries Significantly Affect the
Chemical, Physical, or Biological Integrity of (a)(1) Through (a)(3)
Waters

    Tributaries do not need to flow perennially to have a
significant nexus to downstream waters. Approximately 59% of streams
across the United States (excluding Alaska) flow intermittently or
ephemerally; ephemeral and intermittent streams are particularly
prevalent in the arid and semi-arid Southwest, where they account
for over 81% of streams. Levick et al. 2008. Despite their
intermittent or ephemeral flow, these streams nonetheless perform
the same important ecological and hydrological functions documented
in the scientific literature as perennial streams, through their
movement of water, nutrients, and sediment to downstream waters. Id.
The importance of intermittent and ephemeral streams is documented
in a 2008 peer-reviewed report by EPA's Office of Research and
Development and the U.S. Department of Agriculture's Agricultural
Research Service, which addresses the hydrological and ecological
significance of ephemeral and intermittent streams in the arid and
semi-arid Southwestern United States and their connections to
downstream waters; the report is a state-of-the-art synthesis of
current knowledge of the ecology and hydrology in these systems. Id.
    Intermittent and ephemeral streams are chemically, physically,
and biologically connected to downstream waters, and these
connections have effects downstream. See, e.g., id. In some areas,
stormflows channeled into alluvial floodplain aquifers by
intermittent and ephemeral streams are the major source of annual
streamflow in rivers. Perennial flows are not necessary for chemical
connections. Periodic flows in ephemeral or intermittent tributaries
can have a strong influence on biogeochemistry by connecting the
channel and other landscape elements. See, e.g., Report at 4-16
(citing H.M. Valett, et. al., ``Biogeochemical and Metabolic
Responses to the Flood Pulse in a Semiarid Floodplain,'' Ecology
86(1): 220-234 (2005)). This episodic connection can be very
important for transmitting a substantial amount of material into
downstream rivers. See, e.g., id. (citing Nadeau and Rains (2007)).
Ephemeral desert streams have been shown to export particularly high
sediment loadings. See, e.g., id. at 4-10 (citing M.A. Hassan,
``Observations of Desert Food Bores,'' Earth Surface Processes and
Landforms 15:481-485 (1990)). Ephemeral streams can also temporarily
and effectively store large amounts of sediment that would otherwise
wash downstream, contributing to the maintenance of downstream water
quality and productive fish habitat. See, e.g., S.H. Duncan, et al.,
``Transport of Road-Surface Sediment through Ephemeral Stream
Channels,'' Water Resources Bulletin 23(1): 113-119 (1987). This
temporary storage of sediment thus helps maintain the chemical and
biologic integrity of downstream waters.
    The Report provides case studies of prairie streams and
Southwest intermittent and ephemeral streams, two stream types whose
jurisdictional status has been called into question in the past.
These case studies highlight the importance of these streams to
downstream waters, despite their small size and ephemeral or
intermittent flow regime. Prairie streams are frequently subjected
to the extremes of drying and flooding, and intermittent or flashy
hydrology is prevalent in river networks throughout most of the
Great Plains. Report at 4-40 (citing W.J. Matthews, ``North American
Prairie Streams as Systems for Ecological Study,'' Journal of the
North American Benthological Society 7:387-409 (1988); A.V. Zale et
al., ``The Physicochemistry, Flora, and Fauna of Intermittent
Prairie Streams: A Review of the Literature,'' United States Fish
and Wildlife Service Biological Report 89:1-44 (1989); N.L. Poff,
``A Hydrogeography of Unregulated Streams in the United States and
an Examination of Scale Dependence in Some Hydrological
Descriptors,'' Freshwater Biology 36:71-91 (1996); W.K. Dodds, et
al., ``Life on the Edge: The Ecology of Great Plains Prairie
Streams,'' Bioscience 54:205-216 (2004)). Prairie streams typically
represent a collection of spring-fed, perennial pools and reaches,
embedded within larger, intermittently flowing segments. Id. at 4-55
(citing T.R. Labbe, and K.D. Fausch, ``Dynamics of Intermittent
Stream Habitat Regulate Persistence of a Threatened Fish at Multiple
Scales,'' Ecological Applications 10:1774-1791 (2000)). These
streams have

significant chemical, physical, and biological connections to
downstream waters, despite extensive alteration of historical
prairie regions by agriculture, water impoundment, water
withdrawals, and other human activities, and the challenges these
alterations create for assessing connectivity. Id. (citing W.J.
Matthews, and H.W. Robinson, ``Influence of Drainage Connectivity,
Drainage Area and Regional Species Richness on Fishes of the
Interior Highlands in Arkansas,'' American Midland Naturalist 139:1-
19 (1998); W.K. Dodds, et al., ``Life on the Edge: The Ecology of
Great Plains Prairie Streams,'' Bioscience 54:205-216 (2004)). The
most notable connections are via flood propagation, contaminated
sediment transport, nutrient retention, and the extensive transport
and movement of fish species (including eggs and larvae) throughout
these networks. Id. at 4-55 (citing H.F. Matthai, Floods of June
1965 in South Platte River Basin, Colorado, Water Supply Paper 1850-
B (Washington, DC: U.S. Geological Survey, 1969); A.J. Horowitz, et
al., ``The Effect of Mining on the Sediment-trace Element
Geochemistry of Cores from the Cheyenne River Arm of Lake Oahe,
South Dakota, USA,'' Chemical Geology 67:17-33 (1988); DC Marron,
``The Transport of Mine Tailings as Suspended Sediment in the Belle
Fourche River, West-central South Dakota, USA,'' International
Association of Hydrologic Sciences 184:19-26 (1989); W.K. Dodds, et
al., ``Nitrogen Transport from Tallgrass Prairie Watersheds,''
Journal of Environmental Quality 25:973-981 (1996); K.D. Fausch, and
K.R. Bestgen, ``Ecology of Fishes Indigenous to the Central and
Southwestern Great Plains,'' in F.L. Knopf and F.B. Samson, ed.,
Ecology and Conservation of Great Plains Vertebrates, (New York, NY:
Springer-Verlag, 1997), pp. 131-166; S.P. Platania, and C.S.
Altenbach, ``Reproductive Strategies and Egg Types of Seven Rio
Grande Basin Cyprinids,'' Copeia 1998:559-569 (1998); K.M. Fritz,
and W.K. Dodds, ``Resistance and Resilience of Macroinvertebrate
Assemblages to Drying and Flood in a Tallgrass Prairie Stream
System,'' Hydrobiologia 527:99-112 (2004); K.M. Fritz, and W.K.
Dodds, ``Harshness: Characterization of Intermittent Stream Habitat
over Space and Time,'' Marine and Freshwater Research 56:13-23
(2005); N.R. Franssen, et al., ``Effects of Floods on Fish
Assemblages in an Intermittent Prairie Stream,'' Freshwater Biology
51:2072-2086 (2006); R.B. Alexander, et al., ``Differences in
Phosphorus and Nitrogen Delivery to the Gulf of Mexico from the
Mississippi River Basin,'' Environmental Science & Technology
42:822-830 (2008); J.S. Perkins, and K.B. Gido, ``Stream
Fragmentation Thresholds for a Reproductive Guild of Great Plains
Fishes,'' Fisheries 36:371-383 (2011)).
    Southwestern intermittent and ephemeral streams exert strong
influences on the structure and function of downstream waters, and
the case study (included in the Report) echoes many of the findings
of the functions of intermittent and ephemeral tributaries
generally, which are described above. The case study focuses on the
heavily studied San Pedro River, located in southeast Arizona, in
particular, as a representative example of the hydrological behavior
and the connectivity of rivers in the Southwest, but also examines
evidence relevant to other Southwestern streams. The chemical,
physical, and biological connections of Southwestern intermittent
and ephemeral streams highlighted in the case study are summarized
below. Flows from ephemeral streams are one of the major drivers of
the dynamic hydrology of Southwest rivers (particularly of floods
during monsoon seasons. Id. at 4-60, 4-67 (citing DC Goodrich, et
al., ``Linearity of Basin Response as a Function of Scale in a
Semiarid Watershed,'' Water Resources Research 33:2951-2965 (1997);
F. Yuan, and S. Miyamoto, ``Characteristics of Oxygen-18 and
Deuterium Composition in Waters from the Pecos River in American
Southwest,'' Chemical Geology 255:220-230 (2008)). Downstream river
fishes and invertebrates are adapted to the variable flow regimes
that are influenced strongly by ephemeral tributary systems, which
provide isolated pools as refuges for fish during dry periods. Id.
at 4-68 to 4-69 (citing K.R. John, ``Survival of Fish in
Intermittent Streams of the Chirichua Mountains, Arizona'' Ecology
45:112-119 (1964); T.R. Labbe, and K.D. Fausch, ``Dynamics of
Intermittent Stream Habitat Regulate Persistence of a Threatened
Fish at Multiple Scales,'' Ecological Applications 10:1774-1791
(2000); J.N. Rinne, and D. Miller, ``Hydrology, Geomorphology and
Management: Implications for Sustainability of Native Southwestern
Fishes,'' Reviews in Fisheries Science 14:91-110 (2006); D.A. Lytle,
et al., ``Evolution of Aquatic Insect Behaviors across a Gradient of
Disturbance Predictability,'' Proceedings of the Royal Society--
Series B 275:453-462 (2008)). Ephemeral tributaries in the Southwest
also supply water to mainstem river alluvial aquifers, which aids in
the sustaining river baseflows downstream. Id. at 4-64 (citing DC
Goodrich, et al., ``Linearity of Basin Response as a Function of
Scale in a Semiarid Watershed,'' Water Resources Research 33:2951-
2965 (1997); J.B. Callegary, et al., ``Rapid Estimation of Recharge
Potential in Ephemeral-Stream Channels using Electromagnetic
Methods, and Measurements of Channel and Vegetation
Characteristics,'' Journal of Hydrology 344:17-31 (2007)). Ephemeral
tributaries export sediment downstream during major hydrologic
events; the sediment, in turn, contributes to materials that
comprise alluvial aquifers and shape the fluvial geomorphology (the
science of how rivers and streams form given the landscape setting)
of downstream waters. Id. at 4-65 (citing G.C. Nanson, and J.C.
Croke, ``A Genetic Classification of Floodplains,'' Geomorphology
4:459-486 (1992)). The nutrient and biogeochemical integrity of
downstream Southwestern rivers, such as the San Pedro River, is
heavily influenced by nutrient export from ephemeral tributaries
after storm flow events. Id. at 4-18, 4-66 (citing P.D. Brooks, and
M.M. Lemon, ``Spatial Variability in Dissolved Organic Matter and
Inorganic Nitrogen Concentrations in a Semiarid Stream, San Pedro
River, Arizona,'' Journal of Geophysical Research-Biogeosciences
112:G03S05 (2007)). Extensive downstream river riparian communities
are supported by water, sediment and nutrients exported to the river
from ephemeral tributaries; these riparian communities have a
profound influence on the river attributes through shading,
allochthonous (originating from outside of the channel) inputs of
organic matter, detritus, wood, and invertebrates to the river. Id.
at 4-65 to 4-66 (citing S.V. Gregory, et al., ``An Ecosystem
Perspective of Riparian Zones: Focus on Links between Land and
Water,'' Bioscience 41:540-551 (1991); R.J. Naiman, et al., Riparia:
Ecology, Conservation, and Management of Streamside Communities
(Burlington, MA: Elsevier, Inc., 2005); J.C. Stromberg, et al.,
``Effects of Stream Flow Intermittency on Riparian Vegetation of a
Semiarid Region River (San Pedro River, Arizona),'' River Research
and Applications 21:925-938 (2005), M. Baillie, et al.,
``Quantifying Water Sources to a Semiarid Riparian Ecosystem, San
Pedro River, Arizona,'' Journal of Geophysical Research 112:G03S02
(2007); National Research Council, Riparian Areas: Functions and
Strategies for Management (Washington, DC: National Academy Press,
2002)).

E. Tributary Lakes, Ponds, and Wetlands Significantly Affect the
Chemical, Physical, or Biological Integrity of (a)(1) Through (a)(3)
Waters

    As discussed elsewhere in this preamble, riparian and floodplain
wetlands have a significant nexus to downstream waters, and wetlands
that are tributaries are a subset of such wetlands. The fact that a
wetland tributary is in-stream often enhances its ability to filter
pollutants and contaminants that would otherwise make it downstream;
in-stream wetlands also attenuate floodwaters. Lakes and ponds serve
many important functions that affect the chemical, physical, and
biological conditions downstream. Lake tributaries can act as sinks,
storing floodwaters, sediment, and nutrients, as these materials
have the opportunity to settle out, at least temporarily, as water
moves through the lake to downstream waters. See, e.g., R.W.
Phillips, et al., ``Connectivity and Runoff Dynamics in
Heterogeneous Basins,'' Hydrological Processes 25(19): 3061-3075
(2011). The attenuation of floodwaters can also maintain stream
flows downstream. Id. Lakes, as with other tributaries, can also act
as sources, contributing flow, nutrient, sediment, and other
materials downstream. Total Maximum Daily Loads (TMDLs) for
nutrients have been established for many in-stream lakes across the
country in recognition of the ability of lakes to transport
nutrients downstream, contributing to downstream impairments. See,
e.g. Maine Department of Environmental Protection, Phosphorus
Control Action Plan and Total Maximum Daily (Annual Phosphorous)
Load Report, Daigle Pond, New Canada, Aroostook County, Maine,
Daigle Pond PCAP--TMDL Report, Maine DEPLW--0789 (Maine DEP, 2006);
U.S. Environmental Protection Agency, ``Section 6 Echo Park Lake
TMDLs,'' Los Angeles Area Lakes TMDLs, January 2011 Revised Draft
(2011). Lakes can also serve as habitat for species that then move
downstream. For instance, brook trout that are stocked in headwater

lakes in Idaho and Montana are capable of invading most downstream
habitat, including through very steep channel slopes and waterfalls.
S.B. Adams, et al., ``Geography of Invasion in Mountain Streams:
Consequences of Headwater Lake Fish Introductions,'' Ecosystems
4(4): 296-307. These non-native species can then affect the
biological integrity of downstream waters by impacting populations
of native fish species, such as cutthroat trout, downstream. See,
e.g., J.B. Dunham, et al., ``Alien Invasions in Aquatic Ecosystems:
Toward an Understanding of Brook Trout Invasions and Potential
Impacts on Inland Cutthroat Trout in Western North America,''
Reviews in Fish Biology and Fisheries 12(4): 373-391 (2002). For
example, non-native trout were introduced in headwater tributary
lakes to the Little Kern River in the southern Sierra Nevada and
dispersed downstream, causing the near-extinction of the native
Little Kern golden trout. R.A. Knapp, and K.R. Matthews, ``Effects
on Nonnative Fishes on Wilderness Lake Ecosystems in the Sierra
Nevada and Recommendations for Reducing Impacts,'' in D. N. Cole, et
al., ed., Wilderness Science in a Time of Change Conference, Volume
5: Wilderness Ecosystems, Threats, and Management, Missoula,
Montana, May 23-27, 1999, Proceedings RMRS-P-15-VOL-5 (Ogden, UT:
U.S. Department of Agriculture, Forest Service, Rocky Mountain
Research Station, 2000), 312-317. These studies demonstrate the
ability of organisms to travel from tributary lakes to downstream
waters, which is not limited to just non-native species; many other
species can also move downstream and back again.
    One type of wetlands located in-stream are unidirectional
wetlands that are connected to the river network through a channel
(e.g., wetlands that serve as stream origins; a definition of
``unidirectional wetlands'' can be found in part I section 4.B
above). These tributary wetlands are generally exemplary of
tributary wetlands as a whole, and because the Report focuses in
part on these wetlands, they are discussed here in further detail.
These are wetlands from which a stream channel originates. Report at
5-1 to 5-2. They are part of the stream network itself, and along
with first- and second-order streams, form the headwaters of the
river network. Such wetlands have a direct hydrologic connection to
the tributary network via unidirectional flow from wetland to the
headwater stream. Channel origin wetlands generally have important
chemical, physical, and biological effects on (a)(1) through (a)(3)
waters, including hydrologic, water quality, and habitat functions,
regardless if the outflow from the wetland to the stream is
perennial, intermittent, or ephemeral. Id. Like other wetlands,
wetlands that serve as stream origins can transport channel-forming
sediment and woody debris, transport stored organic matter, remove
and transform pollutants and excess nutrients such as nitrogen and
phosphorus, attenuate and store floodwaters, contribute to stream
baseflow through groundwater recharge, and provide habitat for
breeding fish, amphibians, reptiles, birds, and other aquatic and
semi-aquatic species that move from the wetlands to the river
network. Id. at 5-41.
    Wetlands that serve as stream origins connect via perennial,
intermittent, or ephemeral drainages to river networks. Id. at 5-22
to 5-23 (citing M.C. Rains, et al., ``The Role of Perched Aquifers
in Hydrological Connectivity and Biogeochemical Processes in Vernal
Pool Landscapes, Central Valley, California,'' Hydrological
Processes 20:1157-1175 (2006); M.C. Rains, et al., ``Geological
Control of Physical and Chemical Hydrology in California Vernal
Pools,'' Wetlands 28:347-362 (2008); T.R. Morley, et al., ``The Role
of Headwater Wetlands in Altering Streamflow and Chemistry in a
Maine, USA Catchment,'' Journal of the American Water Resources
Association 47:337-349 (2011)). Regardless of the permanence of
flow, such wetlands have an impact on downstream water. Id. at 5-1
to 5-2. Wetland seeps, for example, can form where groundwater
discharges from breaks in slope. Id. at 5-21 (citing B.R. Hall, et
al., ``Environmental Influences on Plant Species Composition in
Ground-water Seeps in the Catskill Mountains of New York,'' Wetlands
21:125-134 (2001); M.A. O'Driscoll, and D.R. DeWalle, ``Seeps
Regulate Stream Nitrate Concentration in a Forested Appalachian
Catchment,'' Journal of Environmental Quality 39:420-431 (2010)).
They often have perennial connections to the stream, providing
important sources of water downstream, particularly during summer
baseflow. Id. at 5-22 (citing T.R. Morley, et al., ``The Role of
Headwater Wetlands in Altering Streamflow and Chemistry in a Maine,
USA Catchment,'' Journal of the American Water Resources Association
47:337-349 (2011)). In Maine, for example, seeps were found to
provide 40 to 80% of stream water during baseflow periods. Id. In
other cases, surface connections between channel origin wetlands and
streams are intermittent or ephemeral. For example, California
vernal pools spill water a great number of days during the years via
channels, providing water downstream. Id. (citing M.C. Rains, et
al., ``The Role of Perched Aquifers in Hydrological Connectivity and
Biogeochemical Processes in Vernal Pool Landscapes, Central Valley,
California,'' Hydrological Processes 20:1157-1175 (2006); M.C.
Rains, et al., ``Geological Control of Physical and Chemical
Hydrology in California Vernal Pools,'' Wetlands 28:347-362 (2008)).
In addition to surface water connections, groundwater flow can
hydrologically connect wetlands that serve as stream origins with
the stream network. Id. at 5-23.
    The hydrologic connection of the wetland to the stream can
affect streamflow by altering baseflow or storm flow through several
mechanisms, including surface storage and groundwater recharge. Id.
at 5-25. Studies at the larger scale have shown that wetlands, by
storing water, reduce peak streamflows and, thus, downstream
flooding. Id. (citing J. Jacques, and D. L. Lorenz, Techniques for
Estimating the Magnitude and Frequency of Floods of Ungauged Streams
in Minnesota, Report 87-4170 (Washington, DC: U.S. Geological
Survey, 1988); Vining, K.C., Simulation of Streamflow and Wetland
Storage, Starkweather Coulee Subbasin, North Dakota, Water Years
1981-98, Water-Resources Investigations Report 02-4113 (Bismarck,
ND: U.S. Geological Survey, 2002), 33 p.; P. McEachern, et al.,
``Landscape Control of Water Chemistry in Northern Boreal Streams of
Alberta,'' Journal of Hydrology 323:303-324 (2006); R.A. Gleason, et
al. Estimating Water Storage Capacity of Existing and Potentially
Restorable Wetland Depressions in a Subbasin of the Red River of the
North, U.S. Geological Survey Open-File Report 2007-1159 (Reston,
VA: U.S. Geological Survey, 2007), 36 p.). In some cases, however,
where wetlands that serve as stream origins are already saturated
prior to rainfall, they can convey stormwater quickly downstream and
thus actually increase flood peaks. Id. at 227 (citing Bay, R.,
``Runoff from Small Peatland Watersheds,'' Journal of Hydrology
9:90-102 (1969); A. Bullock, and M. Acreman, ``The Role of Wetlands
in the Hydrological Cycle,'' Hydrology and Earth System Sciences
7:358-389 (2003)). This is because the wetland soil, if completely
saturated, cannot store any additional water, making the wetland
enable to store floodwater.
    Wetlands that serve as stream origins have important chemical
connections to downstream waters that affect the integrity of those
waters. These wetlands contain diverse microbial populations that
perform various chemical transformations, acting as source of
compounds and influencing the water quality downstream. Id. at 5-28
(citing K.R. Reddy, and R.D. DeLaune, Biogeochemistry of Wetlands:
Science and Applications, 774 p. (2008)). Sulfate-reducing bacteria
found in some headwater wetlands produce methylated mercury, which
is then transported downstream by surface flows. Id. (citing O.K.
Linqvist, et al., ``Mercury in the Swedish Environment--Recent
Research on Causes, Consequences, and Remedial Measures,'' Water Air
and Soil Pollution 55:xi-xiii (1991); G. Mierle, and R. Ingram,
``The Role of Humic Substances in the Mobilization of Mercury from
Watersheds,'' Water Air and Soil Pollution 56:349-357 (1991); C.T.
Driscoll, et al., ``The Role of Dissolved Organic Carbon in the
Chemistry and Bioavailability of Mercury in Remote Adirondack
Lakes,'' Water Air and Soil Pollution 80:499-508 (1995); B.A.
Branfireun, et al., ``In situ Sulphate Stimulation of Mercury
Methylation in a Boreal Peatland: Toward a Link Between Acid Rain
and Methylmercury Contamination in Remote Environments,'' Global
Biogeochemical Cycles 13:743-750 (1999)). Wetlands, including those
that serve as stream origins, are the principle sources of dissolved
organic carbon (DOC) in forests to downstream waters. Id. (citing
P.J. Mulholland, and E.J. Kuenzler, ``Organic Carbon Export from
Upland and Forested Wetland Watersheds,'' Limnology and Oceanography
24:960-966 (1979); N.R. Urban, et al., ``Export of Dissolved Organic
Carbon and Acidity from Peatlands,'' Water Resources Research
25:1619-1628 (1989); B.W. Eckhardt and T.R. Moore, ``Controls on
Dissolved Organic Carbon Concentrations in Streams of Southern
Quebec,'' Canadian Journal of Fisheries and Aquatic Sciences
47:1537-1544 (1990); J.-F. Koprivnjak and T.R. Moore,

``Sources, Sinks, and Fluxes of Dissolved Organic Carbon in
Subarctic Fen Catchments,'' Arctic and Alpine Research 24:204-210
(1992); P. Kortelainen, ``Content of Total Organic Carbon in Finnish
Lakes and Its Relationship to Catchment Characteristics,'' Canadian
Journal of Fisheries and Aquatic Sciences 50:1477-1483 (1993); T.A.
Clair, et al., ``Exports of Carbon and Nitrogen from River Basins in
Canada's Atlantic Provinces,'' Global Biogeochemical Cycles 8:441-
450 (1994); D. Hope, et al., ``A Review of the Export of Carbon in
River Water: Fluxes and Processes,'' Environmental Pollution 84:301-
324 (1994); P.J. Dillon and L.A. Molot, ``Effects of Landscape Form
on Export of Dissolved Organic Carbon, Iron, and Phosphorus from
Forested Stream Catchments,'' Water Resources Research 33:2591-2600
(1997); S.E. Gergel, et al., ``Dissolved Organic Carbon as an
Indicator of the Scale of Watershed Influence on Lakes and Rivers,''
Ecological Applications 9:1377-1390 (1999)). Export of DOC to
downstream waters supports primary productivity, effects pH and
buffering capacity, and regulates exposure to UV-B radiation. Id. at
5-29 (citing K.N. Eshelman and H.F. Hemond, ``The Role of Organic
Acids in the Acid-base Status of Surface Waters at Bickford
Watershed, Massachusetts,'' Water Resources Research 21:1503-1510
(1985); L.O. Hedin, et al., ``Patterns of Nutrient Loss from
Unpolluted Old-growth Temperate Forests: Evaluation of
Biogeochemical Theory,'' Ecology 76:493-509 (1995); D.W. Schindler
and P.J. Curtis, ``The Role of DOC in Protecting Freshwaters
Subjected to Climate Warming and Acidification from UV Exposure,''
Biogeochemistry 36:1-8 (1997); J.C. Nuff and G.P. Asner, ``Dissolved
Organic Carbon in Terrestrial Ecosystems: Synthesis and a Model,''
Ecosystems 4:29-48 (2001)).
    Wetlands also act as sinks and transformers for pollutants,
including excess nutrients, through such processes as
denitrification, ammonia volatilization, microbial and plant biomass
assimilation, sedimentation, sorption and precipitation, biological
uptake, and long-term storage of plant detritus. Id. (citing K.C.
Ewel and H.T. Odum, Cypress Swamps (Gainesville, FL: University
Presses of Florida, 1984); S.J. Nixon and V.J. Lee, Wetlands and
Water Quality: A Regional Review of Recent Research in the United
States on the Role of Freshwater and Saltwater Wetlands as Sources,
Sinks, and Transformers of Nitrogen, Phosphorus, and Various Heavy
Metals, Technical Report Y-86-2 (Vicksburg, MS: U.S. Army Corps of
Engineers, Waterways Experiment Station, 1986); C. Johnston,
``Sediment and Nutrient Retention by Freshwater Wetlands: Effects on
Surface Water Quality,'' Critical Reviews in Environmental Control
21:491-565 (1991); K.R. Reddy, et al., ``Phosphorus Retention in
Streams and Wetlands: A Review,'' Critical Reviews in Environmental
Science and Technology 29:83-146 (1999); W.J. Mitsch and J.G.
Gosselink, Wetlands, 4th edition (Hoboken, NJ: John Wiley & Sons
Inc., 2007); K.R. Reddy, and R.D. DeLaune, Biogeochemistry of
Wetlands: Science and Applications (Boca Raton, FL: CRC Press,
2008); R.H. Kadlec and S.D. Wallace, Treatment Wetlands, 2nd edition
(Boca Raton, FL: CRC Press, 2009)). Specifically, wetlands reduce
phosphorus, nitrate, and ammonium by large percentages. Id. at 5-30
(citing F.E. Dierberg and P.L. Brezonik, ``Nitrogen and Phosphorus
Mass Balances in a Cypress Dome Receiving Wastewater,'' in K.C. Ewel
and H.T. Odum, ed., Cypress Swamps (Gainesville, FL: University
Presses of Florida, 1984), pp. 112-118; E.J. Dunne, et al.,
``Phosphorus Release and Retention by Soils of Natural Isolated
Wetlands,'' International Journal of Environment and Pollution
28:496-516 (2006); T.E. Jordan, et al., ``Comparing Functional
Assessments of Wetlands to Measurements of Soil Characteristics and
Nitrogen Processing,'' Wetlands 27:479-497 (2007)). These processes
are important for protecting downstream waters from pollutants from
agricultural runoff. Wetland microbial processes reduce other
pollutants, such as pesticides, hydrocarbons, heavy metals, and
chlorinated solvents. Id. (citing R.R. Brooks, et al., ``Cobalt and
Nickel Uptake by the Nyssaceae,'' Taxon 26:197-201 (1977); C.M. Kao,
et al., ``Non-point Source Pesticide Removal by a Mountainous
Wetland,'' Water Science and Technology 46:199-206 (2002); P.I.
Boon, ``Biogeochemistry and Bacterial Ecology of Hydrologically
Dynamic Wetlands,'' in D. P. Batzer and R. R. Sharitz, ed., Ecology
of Freshwater and Estuarine Wetlands (Berkeley, CA: University of
California Press, 2006), pp. 115-176).
    Tributary wetlands have important biological connections
downstream that impact the integrity of (a)(1) through (a)(3)
waters. Emergent and aquatic vegetation found in wetlands disperse
by water, wind, and hitchhiking on migratory animals from tributary
wetlands downstream. Id. at 5-31 (citing M.B. Soons and G.W. Heil,
``Reduced Colonization Capacity in Fragmented Populations of Wind-
Dispersed Grassland Forbs,'' Journal of Ecology 90:1033-1043 (2002);
M.B. Soons, ``Wind Dispersal in Freshwater Wetlands: Knowledge for
Conservation and Restoration,'' Applied Vegetation Science 9:271-278
(2006); C. Nilsson, et al., ``The Role of Hydrochory in Structuring
Riparian and Wetland Vegetation,'' Biological Reviews 85:837-858
(2010)). Similarly, fish move between the river network and wetlands
during times of surface water connections, and tributary wetlands by
definition are connected on the surface to downstream waters. Id. at
5-32 (citing J.W. Snodgrass, et al., ``Factors affecting the
occurrence and structure of fish assemblages in isolated wetlands of
the upper coastal plain, USA,'' Canadian Journal of Fisheries and
Aquatic Sciences 53:443-454 (1996); K.D. Zimmer, et al., ``Effects
of fathead minnow colonization and removal on a prairie wetland
ecosystem,'' Ecosystems 4:346-357 (2001); M.J. Baber, et al.,
``Controls on fish distribution and abundance in temporary
wetlands,'' Canadian Journal of Fisheries and Aquatic Sciences
59:1441-1450 (2002); M.A. Hanson, et al., ``Biotic interactions as
determinants of ecosystem structure in prairie wetlands: An example
using fish,'' Wetlands 25:764-775 (2005); B.R. Herwig, et al.,
``Factors influencing fish distributions in shallow lakes in prairie
and prairie-parkland regions of Minnesota, USA,'' Wetlands 30:609-
619 (2010)). Mammals that can disperse overland can also contribute
to connectivity. Id. (citing C.E. Shanks, and G.C. Arthur, ``Muskrat
movements and population dynamics in Missouri farm ponds and
streams,'' Journal of Wildlife Management 16:138-148 (1952); W.R.
Clark, ``Ecology of muskrats in prairie wetlands,'' in H.R. Murkin,
et al., ed., Prairie Wetland Ecology: The Contribution of the Marsh
Ecology Research Program, (Ames, IA: Iowa State University Press,
2000), pp. 287-313). Insects also hitchhike on birds and mammals
from tributary wetlands to the stream network, which can then serve
as a food source for downstream waters. Id. (citing J. Figuerola,
and A.J. Green, ``Dispersal of Aquatic Organisms by Waterbirds: A
Review of Past Research and Priorities for Future Studies,''
Freshwater Biology 47:483-494 (2002); J. Figuerola, et al.,
``Invertebrate Eggs Can Fly: Evidence of Waterfowl-Mediated Gene
Flow in Aquatic Invertebrates,'' American Naturalist 165:274-280
(2005)). Insects that are flight-capable also use both stream and
tributary wetlands, moving from the stream to the wetland to find
suitable habitat for overwintering, refuge from adverse conditions,
hunting, foraging, or breeding. Id. at 5-33 (citing D.D. Williams,
``Environmental Constraints in Temporary Fresh Waters and Their
Consequences for the Insect Fauna,'' Journal of the North American
Benthological Society 15:634-650 (1996); A.J. Bohonak and D.G.
Jenkins, ``Ecological and Evolutionary Significance of Dispersal by