Freshwater Invertebrates,'' Ecology Letters 6:783-796 (2003)).
Amphibians and reptiles, including frogs, toads, and newts, also
move between streams or rivers and tributary wetlands to satisfy
part of their life history requirements, feed on aquatic insects,
and avoid predators. Id. (citing V.S. Lamoureux and D.M. Madison,
``Overwintering Habitats of Radio-Implanted Green Frogs, Rana
clamitans,'' Journal of Herpetology 33:430-435 (1999); K.J. Babbitt,
et al., ``Patterns of Larval Amphibian Distribution Along a Wetland
Hydroperiod Gradient,'' Canadian Journal of Zoology-Revue Canadienne
De Zoologie 81:1539-1552 (2003); S.B. Adams, et al., ``Instream
Movements by Boreal Toads (Bufo boreas boreas),'' Herpetological
Review 36:27-33 (2005); D.M. Green, ``Bufo americanus, American
Toad,'' in M. Lannoo, ed., Amphibian Declines: The Conservation
Status of United States Species (Berkeley, CA: University of
California Press, 2005), pp. 692-704; T.W. Hunsinger and M.J.
Lannoo, ``Notophthalmus viridescens, Eastern Newt,'' in M. Lannoo,
ed., Amphibian Declines: The Conservation Status of United States
Species (Berkeley, CA: University of California Press, 2005), pp.
912-914; J.W. Petranka, and C.T. Holbrook, ``Wetland Restoration for
Amphibians: Should Local Sites Be Designed to Support
Metapopulations or Patchy Populations?,'' Restoration Ecology
14:404-411 (2006); A.L. Subalusky, et al., ``Ontogenetic Niche
Shifts in the American Alligator Establish Functional Connectivity
between Aquatic Systems,'' Biological Conservation 142:1507-1514
(2009)).
    Lake, pond, and wetland tributaries, including wetlands that
serve as stream origins, have important chemical, physical,

and biological connections downstream that affect (a)(1) through
(a)(3) waters. Their direct hydrologic connection to the stream
network facilitates the significant impact they have downstream.
This impact on downstream waters occurs regardless of whether their
flow is perennial, intermittent, or ephemeral. Thus, lake, pond, and
wetland tributaries serve the same important functions as stream
tributaries, which in turn greatly impact downstream (a)(1) through
(a)(3) waters, particularly when their functional contributions to
the chemical, physical, and biological conditions of downstream
waters are combined at a watershed scale.

F. Man-Made or Man-Altered Tributaries Significantly Affect the
Physical, Chemical and Biological Integrity of (a)(1) Through (a)(3)
Waters

    The agencies' proposed rule clarifies that man-made and man-
altered tributaries as defined in the proposed rule are ``waters of
the United States'' because the significant nexus between a
tributary and a traditional navigable water or interstate water is
not broken where the tributary flows through a culvert or other
structure. Note that the proposal excludes certain ditches from CWA
jurisdiction by rule in paragraphs (b)(3) and (b)(4). The scientific
literature indicates that structures that convey water do not affect
the connectivity between streams and downstream rivers. Indeed,
because such structures can reduce water losses from
evapotranspiration and seepage, such structures likely enhance the
extent of connectivity by more completely conveying the water
downstream.
    Man-made and man-altered tributaries include impoundments,
ditches, canals, channelized streams, piped, and the like. Ditches
and canals are wide-spread across the United States. Ditches may
have been streams that were channelized. They are purposely
constructed to allow the hydrologic flow of the tributary to
continue downstream. Man-made and man-altered tributaries, despite
human manipulation, usually continue to have chemical, physical, or
biological connections downstream and to serve important functions
downstream. Because these tributaries are hydrologically connected
to downstream waters, the chemical and some biological connections
to downstream waters that are supported by this hydrologic
connection are still intact. Often-times man-made tributaries create
connections where they did not previously exist, such as canals that
connect two rivers in different watersheds.
    Tributary ditches and other man-made or man-altered waters that
meet the definition of ``tributary'' have a significant nexus to
(a)(1) through (a)(3) waters due to their impact, either
individually or with other tributaries, on the chemical, physical,
or biological integrity of those downstream waters. Tributary
ditches and the like, as with other tributaries, have chemical,
physical, and biological connections with downstream waters that
substantially impact those waters. Tributary ditches and canals can
have perennial, intermittent, or ephemeral flow. As described above,
tributaries of all flow regimes have a significant nexus to
downstream (a)(1) through (a)(3) waters. Due to the often
straightened and channelized nature of ditches, these tributaries
quickly move water downstream to (a)(1) through (a)(3) waters.
Ditches and canals, like other tributaries, export sediment,
nutrients, and other materials downstream. Due to their often
channelized nature, ditches are very effective at transporting water
and these materials, including nitrogen, downstream. See, e.g., J.P.
Schmidt, et al., ``Nitrogen Export from Coastal Plain Field
Ditches,'' Journal of Soil and Water Conservation 62(4):235-243;
J.S. Strock, et al., ``Managing Natural Processes in Drainage
Ditches for Nonpoint Source Nitrogen Control.'' Journal of Soil and
Water Conservation 62(4): 188-196 (2007). Ditches provide habitat
for fish and other aquatic organisms. See, e.g., P.C. Smiley, Jr.,
et al., ``Contribution of Habitat and Water Quality to the Integrity
of Fish Communities in Agricultural Drainage Ditches,'' Journal of
Soil and Water Conservation 63(6):218A-219A (2008). Fish and other
aquatic organisms utilize canals and ditches to move to different
habitats, sometimes over long distances. F.J. Rahel, ``Biogeographic
Barriers, Connectivity and Homogenization of Freshwater Faunas: It's
a Small World after All,'' Freshwater Biology 52(4): 696-710 (2007).
    These significant connections and functions continue even where
the tributary has a natural or man-made break in its channel, bed
and banks, or OHWM. The presence of a channel, bed and banks, and
OHWM upstream or downstream of the break is an indication that
connections still exist. The significant nexus between a tributary
and a downstream water is not broken where the tributary flows
underground for a portion of its length, such as in karst
topography. The hydrologic connection still exists, meaning that the
chemical and biological connections that are mediated by the
hydrologic connection also still exist. Similarly, flow through
boulder fields does not sever the hydrologic connection. When a
tributary flows through a wetland enroute to another or the same
tributary, the significant nexus still exists even though the bed
and banks or ordinary high watermark is broken for the length of the
wetland. As discussed in Part II, section 1.G. of this appendix, in-
stream wetlands provide numerous benefits downstream, and the
presence of the wetland in stream can provide additional water
quality benefits to the receiving waters. Flow in flat areas with
very low gradients may temporarily break the tributary's bed and
banks or OHWM, but these systems continue to have a significant
nexus downstream. These are just illustrative examples of break in
ordinary high watermark; there are several other types, all of which
do not break the significant nexus between a tributary and the
downstream (a)(1) through (a)(3) water.
    There are more than 80,000 dams in the United States, with over
6,000 exceeding 15 meters in height. Report at 3-48 (citing U.S.
Army Corps of Engineers, National Inventory of Dams (2009)). The
purpose of a dam is to impound (store) water for any of several
reasons (e.g. flood control, human water supply, irrigation,
livestock water supply, energy generation, containment of mine
tailings, recreation or pollution control). See http://www.damsafety.org/layout/subsection.aspx?groupid=14&contentid=47.
Many dams fulfill a combination of the above functions. Because the
purpose of a dam is to retain water effectively and safely, the
water retention ability of a dam is of prime importance. Water may
pass from the reservoir to the downstream side of a dam by: passing
through the main spillway or outlet works; passing over an auxiliary
spillway; overtopping the dam; seepage through the abutments; and
seepage under the dam. Id. All water retention structures are
subject to seepage through their foundations and abutments.
Department of the Army, U.S. Army Corps of Engineers, Engineering
and Design--Design, Construction and Maintenance of Relief Wells, EM
1110-2-1914 (Washington, DC: Department of the Army, 1992), p. 1-1.
Thus waters behind a dam still maintain a hydrologic connection to
downstream waters.
    Numerous studies have shown that dams impede biotic movements,
reducing biological connectivity between upstream and downstream
locations. Report at 3-48 (citing E.A. Greathouse, et al.,
``Indirect Upstream Effects Of Dams: Consequences Of Migratory
Consumer Extirpation In Puerto Rico,'' Ecological Applications 16:
339-352 (2006); C.J. Hall, et al., ``The Historic Influence of Dams
on Diadromous Fish Habitat with a Focus on River Herring and
Hydrologic Longitudinal Connectivity,'' Landscape Ecology 26: 95-
107(2011)). Dams alter but typically do not sever the hydrologic
connection between upstream and downstream waters. (See Part II,
section 2.C. of this appendix). Upstream of large dams riparian
areas are permanently inundated, increasing hydrological
connectivity. Downstream, peak flows and the potential for overbank
lateral flow are reduced; however, dams may also reduce flow
variability downstream, resulting in higher minimum flows and
reduced flow intermittency and thereby increasing hydrological (and
potentially biological) connectivity. Id. (citing N.L. Poff, et al.,
``Homogenization of Regional River Dynamics by Dams and Global
Biodiversity Implications,'' Proceedings of the National Academy of
Sciences of the United States of America 104: 5732-5737 (2007)).
Where an impoundment does stop flow, it also has significant effects
on downstream waters. For example, the downstream segments have a
reduced quantity of waters, less sediment, and reduced species
biological connectivity with upstream refugia.
    Because dams reduce the amount of sediment delivered downstream,
the reservoirs behind dams are actually very effective at retaining
sediment, which can have significant effects in downstream waters.
For instance, the Mississippi River's natural sediment load has been
reduced by an estimated 50% through dam construction in the
Mississippi Basin. M.D. Blum, and H. H. Roberts, ``Drowning of the
Mississippi Delta Due to Insufficient Sediment Supply and Global
Sea-Level Rise,'' Nature Geoscience 2(7): 488-491 (2009).
    Man-made or man-altered tributaries continue to have chemical,
physical, and

biological connections that significantly affect the integrity of
(a)(1) through (a)(3) waters. Though the man-made or man-altered
nature of such tributaries can change the nature of the connections,
it does not eliminate them. Thus, man-made and man-altered
tributaries continue to serve the same important functions as
``natural'' tributaries, which in turn greatly impact downstream
(a)(1) through (a)(3) waters, particularly when their functional
contributions to the chemical, physical, and biological conditions
of downstream waters are combined at a watershed scale.

ii. Adjacent Waters

    Adjacent waters, including adjacent wetlands, alone or in
combination with other adjacent waters in the watershed, have a
substantial impact on the chemical, physical, or biological
integrity of traditional navigable waters, interstate waters, and
the territorial seas. In addition, waters adjacent to tributaries
serve many important functions that directly influence the integrity
of downstream waters including traditional navigable waters,
interstate waters, and the territorial seas. Adjacent waters store
water, which can reduce flooding of downstream waters, and the loss
of adjacent waters has been shown, in some circumstances, to
increase downstream flooding. Adjacent waters maintain water quality
and quantity, trap sediments, store and modify potential pollutants,
and provide habitat for plants and animals, thereby sustaining the
biological productivity of downstream rivers, lakes and estuaries,
which may be traditional navigable waters, interstate waters, or the
territorial seas. The scientific literature and Report supports
these conclusions, as discussed in greater detail below.

1. Adjacent Waters Under This Proposed Rule Have a Significant Nexus to
(a)(1) Through (a)(3) Waters

    The discussion below summarizes the key points made in the
Report and explains the technical basis for supporting a conclusion
that adjacent waters, as defined in this proposed rule, have a
significant nexus to waters identified in paragraphs (a)(1) through
(a)(3) of the proposed rule. The geographic position of an
``adjacent'' water relative to the stream is indicative of the
relationship they share, with many of its defining characteristics
resulting from the movement of materials and energy between the two.
A review and analysis of the scientific literature supports the
conclusion that individually or in combination with similarly
situated waters in a watershed, adjacent waters have a significant
effect on the chemical, physical, and biological integrity of
downstream traditionally navigable waters, interstate waters, and
the territorial seas.

a. Riparian and Floodplain Waters Significantly Affect the Chemical,
Physical, or Biological Integrity of (a)(1) Through (a)(3) Waters

    Waters, including wetlands, often lie within landscape settings
that have bidirectional hydrological exchange with (a)(1) through
(a)(5) waters (e.g., wetlands and open waters in riparian areas and
flood plains). Such waters play an integral role in the chemical,
physical, and biological integrity of the waters to which they are
adjacent. Riparian areas and floodplains often describe the same
geographic region. Report at 3-4. Therefore, the discussion of the
functions of waters, including wetlands, in riparian areas will
typically apply to floodplains unless otherwise noted. Where
connections arise specifically from the act of inundation of
adjacent land during times of higher-than-normal water, the term
``floodplain'' is solely used to describe the area.
    Riparian areas are transition zones between terrestrial and
aquatic ecosystems that are distinguished by gradients in
biophysical conditions, ecological processes, and biota. Id., Report
at 31. Waters including wetlands in riparian areas significantly
influence exchanges of energy and matter with aquatic ecosystems.
See, e.g., id. (citing National Research Council, Riparian Areas:
Functions and Strategies for Management (Washington, DC: The
National Academies Press, 2002).
    Floodplains are low gradient areas bordering stream or river
channels, lakes, and impoundments that were formed by sediment
deposition from those waters under present climatic conditions.
These natural geomorphic features are inundated during moderate to
high water events. Id. (citing L.B. Leopold, A View of the River
(Cambridge, MA: Harvard University Press, 1994); W.R. Osterkamp,
Annotated Definitions of Selected Geomorphic Terms and Related Terms
of Hydrology, Sedimentology, Soil Science and Ecology, USGS Open
File Report 2008-1217 (Reston, VA: U.S. Department of the Interior,
U.S. Geological Survey, 2008)). By ``present climactic conditions,''
the agencies mean that currently or recently active floodplains will
be used to help determine whether wetlands or waters are adjacent to
``waters of the United States.'' The proposed definition is limited
to the present climactic conditions in order to best represent the
floodplain that has an active and significant relationship with the
stream or river channel. Historic floodplains that played a role in
the river or lake dynamics in the past only will not be used to
determine whether a water is adjacent. Floodplains formed under
different climactic conditions that no longer connect to the stream
channel that formed them are terraces. Id. It should be noted that
``floodplain'' as defined in today's proposed rule does not
necessarily equate to the 100-year floodplain as defined by the
Federal Emergency Management Agency (FEMA). However, the FEMA
defined floodplain may often coincide with the current definition
proposed in this rule. Flood insurance rate maps are based on the
probability of a flood event occurring (e.g., 100-year floods have a
1% probability of occurring in a given year or 500 year-floods have
a 0.2% probability of occurring in a particular year). Flood
insurance rate maps are not based on an ecological definition of the
term ``floodplain,'' and therefore may not be appropriate for
identifying adjacent wetlands and waters for the purposes of CWA
jurisdiction. Flood insurance rate maps are developed by applying
models and other information to identify areas that would be
inundated by a flood event of a particular probability of recurring.
    Riparian waters take many different forms. Some may be wetlands,
which are defined in paragraph (c)(6) of the proposed rule. Others
may be ponds, oxbow lakes, or other types of open waters. Oxbow
lakes, commonly found in floodplains, are formed when river meanders
are cutoff from the rest of the river. Id. at 5-42.

b. Riparian and Floodplain Waters Significantly Affect the Physical
Integrity of (a)(1) Through (a)(3) Waters

    Scientific research shows waters and wetlands in riparian areas
and floodplains to be important in protecting the physical integrity
of aquatic resources. Because riparian and floodplain waters exhibit
bidirectional exchange of water with the waters to which they are
adjacent, they play an important role in determining the volume and
duration of stream flow. Riparian and floodplain waters also have an
essential role in regulating and stabilizing sediment transport to
downstream waters. These characteristics are fundamental to the
physical integrity of streams as well as downstream traditional
navigable waters, interstate waters, and the territorial seas.
    Riparian and floodplain wetlands are important for the reduction
or delay of floods. Id.at 3-22 (citing A. Bullock and M. Acreman,
``The Role of Wetlands in the Hydrological Cycle,'' Hydrology and
Earth System Sciences 7:358-389 (2003)). Waters in riparian areas
control flooding during times of high precipitation or snowmelt by
capturing water from overbank flow and storing excess stream water.
Id. at 5-6. One study found that peak flows in the Cache River in
Arkansas decreased by 10-20% mainly because of floodplain water
storage. Id. (citing R. Walton, et al., ``Hydrology of the Black
Swamp Wetlands on the Cache River, Arkansas,'' Wetlands 16:279-287
(1996). Research has shown that floodplain wetlands in Ohio store
about 40% of the flow of small streams. Id. at 5-6 to 5-7 (citing
D.E. Gamble, et al., An Ecological and Functional Assessment of
Urban Wetlands in Central Ohio. Columbus, Ohio, EPA Technical Report
WET/2007-3B, (Columbus, OH: Ohio Environmental Protection Agency,
Wetland Ecology Group, Division of Surface Water, 2007)). These and
similar findings point to the close hydrological influence that
waters in riparian and floodplain areas have on streams.
    Some adjacent waters are bordering or contiguous with (a)(1)
through (a)(5) waters. Because of their close physical proximity to
nearby water bodies, they readily exchange their waters through the
saturated soils surrounding the stream or through surface exchange.
This commingling of waters allows bordering or contiguous waters to
both provide chemically transformed waters to streams and to absorb
excess stream flow.
    Flow between neighboring waters and streams is more longitudinal
(downslope) at headwaters and more lateral further downstream. Id.
at 5-38, Table 5-3. These connections in part determine stream flow
volume and duration. Waters, including wetlands, in riparian areas
connect to neighboring water bodies through various surface and
subsurface connections. See, e.g., id. at 3-4 (citing National
Research Council,

Riparian Areas: Functions and Strategies for Management (Washington,
DC: National Academy Press, 2002)). Floodplains, similarly, are
closely associated with the groundwater found beneath and beside
river channels (which are considered shallow aquifers) and waters in
floodplains readily exchange water with such aquifers. Id. at 3-14
(citing J.A. Stanford and J. V. Ward, ``An Ecosystem Perspective of
Alluvial Rivers: Connectivity and the Hyporheic Corridor,'' Journal
of the North American Benthological Society 12:48-60 (1993); C.
Amoros and G. Bornette, ``Connectivity and Biocompexity in
Waterbodies of Riverine Floodplains,'' Freshwater Biology 47:761-776
(2002); G.C. Poole, et al., ``Multiscale Geomorphic Drivers of
Groundwater Flow Paths: Subsurface Hydrologic Dynamics and Hyporheic
Diversity,'' Journal of the North American Benthological Society
25:288-303 (2006)). Riparian and floodplain wetlands are frequently
contiguous with streams and other water bodies and significantly
influence the hydrology of such water bodies. Id. at 5-6 (citing
R.J. Naiman, et al., Riparia: Ecology, Conservation, and Management
of Streamside Communities (Burlington, MA: Elsevier Academic Press,
2005); P. Vidon, et al., ``Hot Spots and Hot Moments in Riparian
Zones: Potential for Improved Water Quality Management,'' Journal of
the American Water Resources Association 46:278-298 (2010)).
Floodplain wetlands are important for the reduction or delay of
floods. Id. (citing A. Bullock and M. Acreman, ``The Role of
Wetlands in the Hydrological Cycle,'' Hydrology and Earth System
Sciences 7:358-389 (2003)). Oxbow lakes also retain flood waters.
Id. at 5-44. Adjacent ponds generally function similarly to oxbow
lakes.
    Waters in riparian areas filter sediment washed down from
uplands and collect sediment from overbank flow as the river or
stream floods. Id. at 5-7. For example, riparian areas were observed
to collect 80-90% of the sediment from farmlands in a study in North
Carolina. Id. (citing 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)). Maintaining the equilibrium between sediment deposition
and sediment transport is important to maintain the physical shape
and structure of stream channels. Significant changes to upstream
channels can affect the chemical, physical, and biological condition
of downstream (a)(1) through (a)(3) waters.
    The physical effects of excess sediment can impair chemical and
ecological integrity in a variety of ways. Id. at 5-9 (citing P.J.
Wood and P.D. Armitage, ``Biological Effects of Fine Sediment in the
Lotic Environment,'' Environmental Management 21:203-217 (1997)).
Excess sediment is linked to increasing contaminant and nutrient
concentrations, all of which tributaries can transmit downstream,
affecting water quality. Excess sediment may block and absorb
sunlight transmission through the water column, inhibiting plant
photosynthesis and warming the water in the stream. Sediment may
fill the interstitial spaces between rocks in a streambed, which
many fish and aquatic species use for mating, reproduction, and
shelter from predators. This kind of physical degradation of
tributary streambeds results in less suitable habitat available for
animals and fish that move between upstream and downstream waters.
Riparian waters that retain sediments thus protect downstream waters
from the effects of excess sediment.
    Oxbow lakes play similar roles in the floodplain as they are an
integral part of alluvial floodplains of meandering rivers. Id. at
5-42 (citing K.O. Winemiller, et al., ``Fish Assemblage Structure in
Relation to Environmental Variation among Brazos River Oxbow
Lakes,'' Transactions of the American Fisheries Society 129:451-468
(2000), K. Glinska-Lewczuk, ``Water Quality Dynamics of Oxbow Lakes
in Young Glacial Landscape of NE Poland in Relation to Their
Hydrological Connectivity,'' Ecological Engineering 35:25-37
(2009)). They connect to rivers by periodic overland flow, typically
from the river during flooding events, and bidirectional shallow
subsurface flow through fine river soils (bidirectional means flow
from river to lake and lake to river). Id. at 5-43 to 5-44. Oxbow
lakes generally have an important influence on the condition and
function of rivers. Id. at 5-48 to 5-49. That influence can vary
with the distance from the river and the age of the oxbow,
reflecting the frequency and nature of the exchange of materials
that takes place between the two water bodies.
    Because adjacent waters support riparian vegetation, they affect
the capacity of riparian vegetation to influence stream flow,
morphology, and habitat provided in the nearby water body.
Vegetation in riparian waters influences the amount of water in the
stream by capturing and transpiring stream flow and intercepting
groundwater and overland flow. Id. at 3-22, 5-7 (citing P. Meyboom,
``Three Observations on Streamflow Depletion by Phreatophytes,''
Journal of Hydrology 2:248-261 (1964)). Riparian vegetation in
adjacent waters also reduces stream bank erosion, serving to
maintain the physical integrity of the channel. See, e.g., id. at 5-
8 (citing C.E. Beeson and P. F. Doyle, ``Comparison of Bank Erosion
at Vegetated and Non-Vegetated Channel Bends,'' Journal of the
American Water Resources Association 31:983-990 (1995)). In
addition, inputs of woody debris from aquatic vegetation into waters
make important contributions to the channel's geomorphology and the
stream's aquatic habitat value. Id. (citing N.H. Anderson and J. R.
Sedell, ``Detritus Processing by Macroinvertebrates in Stream
Ecosystems,'' Annual Review of Entomology 24:351-377 (1979); M.E.
Harmon, et al., ``Ecology of Coarse Woody Debris in Temperature
Ecosystems,'' Advances in Ecological Research 15:133-302 (1986); F.
Nakamura and F. J. Swanson, ``Effects of Coarse Woody Debris on
Morphology and Sediment Storage of a Mountain Stream System in
Western Oregon,'' Earth Surface Processes and Landforms 18:43-61
(1993); T.E. Abbe and D. R. Montgomery, ``Large Woody Debris Jams,
Channel Hydraulics and Habitat Formation in Large Rivers,''
Regulated Rivers: Research & Management 12:201-221 (1996); R.J.
Naiman and H. Decamps, ``The Ecology of Interfaces: Riparian
Zones,'' Annual Review of Ecology and Systematics 28:621-658 91997);
A.M. Gurnell, et al., ``Large Wood and Fluvial Processes,''
Freshwater Biology 47:601-619 (2002)). Also, the riparian vegetation
that overhangs streams provides shade, providing a critically
important function of reducing fluctuations in water temperature
helping to reduce excessive algal production and to maintain life-
supporting oxygen levels in streams and other waters. Id. at 5-9
(citing S.V. Gregory, et al., ``An Ecosystem Perspective of Riparian
Zones: Focus on Links between Land and Water,'' Bioscience 41:540-
551 (1991); E.C. Volkmar and R.A. Dahlgren, ``Biological Oxygen
Demand Dynamics in the Lower San Joaquin River, California,''
Environmental Science & Technology 40:5653-5660 (2006)). Even small
changes in water temperature can have significant impacts on the
type and number of species present in waters, with higher
temperatures generally associated with degraded habitat which
supports only those species that can tolerate higher temperatures
and reduced levels of dissolved oxygen. Higher water temperatures
are associated with streams and rivers with less valuable
recreational and commercial fisheries. As discussed below, these
physical characteristics of headwater streams influence what types
of organisms live in the region.
    Headwaters and nearby wetlands supply downstream waters with
dissolved organic carbon as a result of decomposition processes from
dead organic matter such as plants. The biological consequences of
this dissolved organic carbon are discussed in more detail below.
The presence of dissolved organic carbon can affect how light
penetrates the water, an important factor in the growth of plants,
algae, and other primary producers, and can protect aquatic
organisms from the harmful effects of UV-B radiation. Id. at 5-28 to
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); J.E. Hobbie and R.G. Wetzel, ``Microbial control of
dissolved organic carbon in lakes: Research for the future,''
Hydrobiologia 229:169-180 (1992); 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); K.R. Reddy and R.D. DeLaune, Biogeochemistry of Wetlands:
Science and Applications, (Boca Raton, FL: CRC Press, 2008)).

c. Riparian and Floodplain Waters Significantly Affect the Chemical
Integrity of (a)(1) Through (a)(3) Waters

    As stated above in the section on tributaries, pollutants such
as petroleum waste products and other harmful pollutants dumped into
any part of the tributary system are likely to flow downstream, or
to be washed downstream, and thereby pollute traditional navigable
waters, interstate

waters, and the territorial seas from which American citizens take
their drinking water, shellfish, fin fish, water-based recreation,
and many other uses. Some wetlands perform the valuable function of
trapping or filtering out some pollutants (such as fertilizers,
silt, and some pesticides), thereby reducing the likelihood that
those pollutants will reach and pollute the tributaries of the
downstream navigable or interstate waters (and eventually pollute
those downstream waters themselves). However, many other pollutants
(such as petroleum wastes and toxic chemical wastes), if dumped into
wetlands or other waters that are adjacent to tributary streams, may
reach those tributaries themselves, and thereafter flow downstream
to pollute the nation's drinking water supply, fisheries, and
recreation areas.
    Riparian and floodplain waters play a critical role in
controlling the chemicals that enter streams and other ``waters of
the United States'' and as a result are vital in protecting the
chemical, physical, and biological integrity of downstream (a)(1)
through (a)(3) waters. Runoff (the water that has not evaporated or
infiltrated into the groundwater) from uplands is a large source of
pollution, but research has shown that wetlands and other riparian
waters trap and chemically transform a substantial amount of the
nutrients, pesticides, and other pollutants before they enter
streams, river, lakes and other waters.
    Chemicals and other pollutants enter waters from point sources,
non-point sources, atmospheric deposition, upstream reaches, and
through the hyporheic zone, a region beneath and alongside a stream
bed where surface water and shallow groundwater mix. Id. at 5-10
(citing SW. 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 Corp of
Engineers, Waterways Experiment Station, 1986); D.F. Whigham and
T.E. Jordan, ``Isolated Wetlands and Water Quality,'' Wetlands
23:541-549 (2003); S.L.Whitmire and S.K. Hamilton, ``Rates of
Anaerobic Microbial Metabolism in Wetlands of Divergent Hydrology on
a Glacial Landscape,'' Wetlands 28:703-714 (2008)). Throughout the
stream network, but especially in headwater streams and their
adjacent wetlands, chemicals are sequestered, assimilated,
transformed, or lost to the atmosphere by microbes, fungi, algae,
and macrophytes present in riparian waters and soils. Id. (citing
SW. 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 Corp 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); 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;
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). These chemical processes reduce or eliminate
pollution that would otherwise enter streams, rivers, lakes and
other waters and subsequently downstream traditional navigable
waters, interstate waters, or the territorial seas. The removal of
the nutrients nitrogen and phosphorus is a particularly important
role for riparian waters. Nutrients are necessary to support aquatic
life, but the presence of excess nutrients can lead to
eutrophication and the depletion of oxygen nearby waters and in
waters far downstream. See, e.g., id. at 1-8. Eutrophication is a
large problem in waters across the United States including such
significant ecosystems as the Chesapeake Bay and Lake Spokane in
Washington. W.M. Kemp, et al., ``Eutrophication of Chesapeake Bay:
Historical Trends and Ecological Interactions,'' Marine Ecology
Progress Series 303(21):1-29 (2005); D.J. Moore and J. Ross, Spokane
River and Lake Spokane Dissolved Oxygen Total Maximum Daily Load:
Water Quality Improvement Report, Publication No. 07-10-073
(Spokane, WA: Washington State Department of Ecology, 2010); R.R.
Murphy, et al., ``Long-Term Trends in Chesapeake Bay Seasonal
Hypoxia, Stratification, and Nutrient Loading,'' Estuaries and
Coasts 34(6):1293-1309 (2011). Eutrophication is the process by
which plants and algae grow in waters to such an extent that the
abundance of vegetation monopolizes the available oxygen,
detrimentally affecting other aquatic organisms. Id. Oxbow lakes
also have high mineralization rates, suggesting that similar to
adjacent wetlands they process and trap nutrients from runoff.
Report at 5-45 to 5-46 (citing K.O. Winemiller, et al., ``Fish
Assemblage Structure in Relation to Environmental Variation among
Brazos River Oxbow Lakes,'' Transactions of the American Fisheries
Society 129:451-468 (2000)). Protection of these waters therefore
helps maintain the chemical integrity of the nation's waters.
    The removal of nitrogen is an important function of all waters,
including wetlands, in the riparian areas. Riparian areas regularly
remove more than half of dissolved nitrogen found in surface and
subsurface water by plant uptake and microbial transformation. Id.
at 5-11 (citing P. Vidon, et al., ``Hot Spots and Hot Moments in
Riparian Zones: Potential for Improved Water Quality Management,''
Journal of the American Water Resources Association 46:278-298
(2010)). Denitrification in surface and subsurface flows is highest
where there is high organic matter and/or anoxic conditions. Id.
Denitrification occurs in wetland soils where there is high organic
matter, low oxygen, denitrifying microbes, and saturated soil
conditions, and rates increase with proximity to streams. Id.
(citing S.V. Gregory, et al., ``An Ecosystem Perspective of Riparian
Zones: Focus on Links between Land and Water,'' Bioscience 41:540-
551 (1991); P. Vidon, et al., ``Hot Spots and Hot Moments in
Riparian Zones: Potential for Improved Water Quality Management,''
Journal of the American Water Resources Association 46:278-298
(2010)). Riparian waters are therefore important in maintaining the
conditions important for denitrification, which in turn protects
streams, rivers, lakes and other waters from nitrogen pollution.
    Plant uptake of dissolved nitrogen in subsurface flows also
accounts for large quantities of nitrogen removal. Riparian forests
have been found to remove 75% of dissolved nitrate transported from
agricultural fields in Maryland. Id. (citing P. Vidon, et al., ``Hot
Spots and Hot Moments in Riparian Zones: Potential for Improved
Water Quality Management,'' Journal of the American Water Resources
Association 46:278-298 (2010)). Likewise, riparian forests in
Georgia remove 65% of nitrogen and 30% of phosphorus from
agricultural sources. Id. at 5-11 to 5-12 (citing Vidon, et al.
2010). A Pennsylvania forest removed 26% of the nitrate from the
subsurface. Id. at 5-12 (citing J.D. Newbold, et al., ``Water
Quality Functions of a 15-Year-Old Riparian Forest Buffer System,''
Journal of the American Water Resources Association 46:299-310
(2010)). The vegetation associated with riparian waters also removes
nitrogen from subsurface flows. Therefore, the conservation of
riparian waters helps protect downstream waters from influxes of
dissolved nitrogen.
    Phosphorus is another potentially harmful nutrient that is
captured and processed in riparian waters. Id. (citing T.A. Dillaha
and S.P. Inamdar, ``Buffer Zones as Sediment Traps or Sources,'' in
N.E. Haycock, T.P. Burt, K.W.T. Goulding, and G. Pinay, ed., Buffer
Zones: Their Processess and Potential in Water Protection,
Proceedings of the International Conference on Buffer Zones,
September 1996 (Hertfordshire, UK: Quest Environmental, 1997), pp.
33-42; A.N. Sharpley and S. Rekolainen, ``Phosphorus in Agriculture
and Its Environmental Implications,'' in H. Tunney, et al., ed.,
Phosphorus Losses from Soil to Water (Cambridge, UK: CAB
International, 1997), pp. 1-54; G.C. Carlyle and A.R. Hill,
``Groundwater Phosphate Dynamics in a River Riparian Zone: Effects
of Hydrologic Flowpaths, Lithology, and Redox Chemistry,'' Journal
of Hydrology 247:151-168 (2001)). Biogeochemical processes,
sedimentation, and plant uptake account for high rates of removal of
particulate phosphorus in riparian areas. Id. (citing C.C. Hoffmann,
et al., ``Phosphorus Retention in Riparian Buffers: Review of Their
Efficiency,'' Journal of Environmental Quality 38:1942-1955 (2009)).
The amount of contact the water has with nearby soils determines the
ability of the riparian area to remove phosphorus. Id. This function
of upstream riparian waters is crucial for maintaining the chemical
and biological integrity of the waters to which they are adjacent,
and for preventing eutrophication in downstream traditional
navigable waters, interstate waters, and the territorial seas.

d. Riparian and Floodplain Waters Significantly Affect the Biological
Integrity of (a)(1) Through (a)(3) Waters

    Waters and wetlands located in both riparian areas and
floodplains support the biological integrity of downstream (a)(1)
through (a)(3) waters in a variety of ways. They provide habitat for
aquatic and water-tolerant plants, invertebrates, and vertebrates,
and provide feeding, refuge, and breeding areas for invertebrates
and fish. Seeds, plants, and animals move between waters in the
riparian zone and floodplains and the adjacent streams, and from
there colonize or utilize downstream waters, including traditional
navigable waters.
    Organic matter from adjacent wetlands is critical to aquatic
food webs, particularly in headwaters, where it is the primary
source of energy flow due to low light conditions that inhibit
photosynthesis. Id. at 5-13 (citing J.L. Tank, et al., ``A Review of
Allochthonous Organic Matter Dynamics and Metabolism in Streams,''
Journal of the North American Benthological Society 29:118-146
(2010)). Headwater streams tend to be located in heavily vegetated
areas compared to larger waters, so they are more likely to contain
leaf litter, dead and decaying plants, and other organic matter that
forms the basis of headwater food webs. The organic matter is
processed by microbes and insects that make the energy available to
higher levels of stream life such as amphibians and fish. Studies
have shown that macroinvertebrates rely on leaf inputs in headwater
streams and that excluding organic litter from a stream resulted in
significant changes to the food web at multiple levels. Id. (citing
G.W. Minshall, ``Role of Allochthonous Detritus in the Tropic
Structure of a Woodland Springbrook Community,'' Ecology 48:139-149
(1967); J.B. Wallace, et al., ``Multiple Trophic Levels of a Forest
Stream Linked to Terrestrial Litter Inputs,'' Science 277:102-104
(1997); J.L. Meyer, et al., ``Leaf Litter as a Source of Dissolved
Organic Carbon in Streams,'' Ecosystems 1:240-249 (1998)). Fish and
amphibian species found in headwaters travel downstream and in turn
become part of the food web for larger aquatic organisms in rivers
and other waters. Organic material provided by riparian waters to
small, headwater streams is therefore important not only to the
small streams that directly utilize this source of energy to support
their biological populations but also to the overall biological
integrity of downstream waters that also benefit from the movement
of fish and other species that contribute to the food web of larger
streams and rivers.
    Floodplain water bodies, including oxbow lakes, accumulate
organic carbon, an important function influenced by the size and
frequency of floods from adjacent rivers. See, e.g., id. at 5-45
(citing A. Cabezas, et al., ``Changing Patterns of Organic Carbon
and Nitrogen Accretion on the Middle Ebro Floodplain (NE Spain),''
Ecological Engineering 35:1547-1558 (2009)). These stored chemicals
are available for exchange with river water when hydrological
connections form. Organic materials are the basis for the food web
in stream reaches where photosynthetic production of energy is
absent or limited, particularly in headwater systems where
vegetative litter alone makes up the base of the aquatic food web.
The maintenance of floodplain waters is therefore an important
component of protecting the biological integrity of downstream
waters into which the headwaters flow.
    The waters, including wetlands, in the riparian area play an
important role in the removal of pesticides. Id. at 5-14 (citing P.
Vidon, et al., ``Hot Spots and Hot Moments in Riparian Zones:
Potential for Improved Water Quality Management,'' Journal of the
American Water Resources Association 46:278-298 (2010). Microbes
near plant roots break down these pesticides. See, e.g., id. (citing
G. Voos, and P.M. Groffman, ``Relationships between microbial
biomass and dissipation of 2,4-D and dicamba in soil,'' Biology and
Fertility of Soils 24:106-110 (1996)). Uptake by aquatic plants has
also been shown to be an important mechanism of removal of the
pesticides alachlor and atrazine. Id. (citing K.G. Paterson and J.L.
Schnoor, ``Fate of Alachlor and Atrazine in a Riparian Zone Field
Site,'' Water Environment Research 64:274-283 (1992)). Riparian
waters also trap and hold pesticide contaminated runoff preventing
it from harming neighboring waters.
    Riparian areas are dynamic places that support a diversity of
aquatic, amphibious, and terrestrial species adapted to the unique
habitat created by periodic flooding events. Id. at 5-15 (citing
W.J. Junk, et al., ``The flood pulse concept in river-floodplain
systems,'' in D.P. Dodge, ed., Proceedings of the International
Large River Symposium Ottawa (Ottawa, Canada: Canadian Special
Publication of Fisheries and Aquatic Sciences 106, 1989), pp. 110-
127; K. Tockner, et al., ``An Extension of the Flood Pulse
Concept,'' Hydrological Processes 14:2861-2883 (2000); C.T.
Robinson, et al., ``The Fauna of Dynamic Riverine Landscapes,''
Freshwater Biology 47:661-677 (2002)). Plants, invertebrates, and
vertebrates use waters, including wetlands, in the riparian areas
for habitat, nutrients, and breeding. As a result, the waters,
including wetlands, in the riparian areas act as sources of
organisms, particularly during inundation events, replenishing
neighboring waters with organisms, seeds, and organic matter.
Inundation and hydrological connectivity of riparian areas greatly
increase the area of aquatic habitats and species diversity. Id. at
5-15 to 5-16 (citing W.J. Junk et al. 1989; R. Jansson, et al.,
``Hydrochory Increases Riparian Plant Species Richness: A Comparison
between a Free-Flowing and a Regulated River,'' Journal of Ecology
93:1094-1103 (2005)). Aquatic animals, including amphibians and
fish, take advantage of the waters present in riparian areas, either
inhabiting them or moving between the riparian water and neighboring
waters. Id. at 5-15, 5-17, 5-19 (citing G.H. Copp, ``The habitat
diversity and fish reproductive function of floodplain ecosystems,''
Environmental Biology of Fishes 26:1-27 (1989); L.A. Smock, et al.,
``Lotic macroinvertebrate production in three dimensions: Channel
surface, hyporheic, and floodplain environments,'' Ecology 73:876-
886 (1992); L.A. Smock, ``Movements of invertebrates between stream
channels and forested floodplains,'' Journal of the North American
Benthological Society 13:524-531 (1994); C. T. Robinson, et al.,
``The fauna of dynamic riverine landscapes,'' Freshwater Biology
47:661-677 (2002); J.S. Richardson, et al., ``Riparian communities
associated with Pacific Northwest headwater streams: Assemblages,
processes, and uniqueness,'' Journal of the American Water Resources
Association 41:935-947 (2005); C. Ilg, et al., ``Long-term reactions
of plants and macroinvertebrates to extreme floods in floodplain
grasslands,'' Ecology 89:2392-2398 (2008); D.E. Shoup, and D. H.
Wahl, ``Fish diversity and abundance in relation to interannual and
lakespecific variation in abiotic characteristics of floodplain
lakes of the lower Kaskaskia River, Illinois,'' Transactions of the
American Fisheries Society 138:1076-1092 (2009)). Likewise, seeds,
plant fragments, and whole plants move between riparian and
floodplain waters and the river network. Id. at 5-15 (citing R.L.
Schneider, and R.R. Sharitz, ``Hydrochory and regeneration in a bald
cypress water tupelo swamp forest,'' Ecology 69:1055-1063 (1988); B.
Middleton, ``Hydrochory, seed banks, and regeneration dynamics along
the landscape boundaries of a forested wetland,'' Plant Ecology
146:169-184 (2000); C. Nilsson, et al., ``The role of hydrochory in
structuring riparian and wetland vegetation,'' Biological Reviews
85:837-858 (2010)).
    Hydrological connections are often drivers of biological
connections, and flooding events enhance the existing connections
between floodplain waters and the river network. As a result, waters
within floodplains have important functions for aquatic health. Many
species have cycles timed to flooding events, particularly in
circumstances where flooding is associated with annual spring
snowmelt or high precipitation. Id. at 5-15 to 5-17, 5-20 (citing
J.R. Thomas, et al., ``A landscape perspective of the stream
corridor invasion and habitat characteristics of an exotic
(Dioscorea oppositifolia) in a pristine watershed in Illinois,''
Biological Invasions 8:1103-1113 (2006); L.M. Tronstad, et al.,
``Aerial colonization and growth: Rapid invertebrate responses to
temporary aquatic habitats in a river floodplain,'' Journal of the
North American Benthological Society 26:460-471 (2007); A. Gurnell,
et al., ``Propagule deposition along river margins: Linking
hydrology and ecology,'' Journal of Ecology 96:553-565 (2008)).
Waters within floodplains act as sinks of seeds, plant fragments,
and invertebrate eggs, allowing for cross-breeding and resulting
gene flow across time. Id. at 5-19 to 5-21 (citing K.M. Jenkins, and
A.J. Boulton, ``Connectivity in a dryland river: Short-term aquatic
microinvertebrate recruitment following floodplain inundation,''
Ecology 84:2708-2723 (2003); D. Frisch, and S.T. Threlkeld, ``Flood-
mediated dispersal versus hatching: Early recolonisation strategies
of copepods in floodplain ponds,'' Freshwater Biology 50:323-330
(2005); B. Vanschoenwinkel, et al., ``Wind mediated dispersal of
freshwater invertebrates in a rock pool metacommunity: Differences
in dispersal capacities and modes,'' Hydrobiologia 635:363-372
(2009)).

Micro- and macroinvertebrates colonize nutrient rich waters within
floodplains during periods of inundation, facilitating an increase
in population and sustaining them though times of limited resources
and population decline. Id. at 5-19 (citing W.J. Junk, et al., ``The
flood pulse concept in river-floodplain systems,'' in D.P. Dodge,
ed., Proceedings of the International Large River Symposium Ottawa
(Ottawa, Canada: Canadian Special Publication of Fisheries and
Aquatic Sciences 106, 1989), pp. 110-127; B. Malmqvist, ``Aquatic
invertebrates in riverine landscapes,'' Freshwater Biology 47:679-
694 (2002); C. Ilg, et al., ``Long-term reactions of plants and
macroinvertebrates to extreme floods in floodplain grasslands,''
Ecology 89:2392-2398 (2008)). Such animals are adapted to high
floods, desiccation (drying out), or other stresses that come with
these regular, systemic fluctuations. Id. at 5-20 (citing Jenkins
and Boulton 2003). Floodplain waters therefore maintain various
biological populations, which periodically replenish adjacent
jurisdictional waters, serving to maintain their biological
integrity.
    Plants and animals use waters, including wetlands, in the
riparian areas and floodplains for habitat, food, and breeding.
Oxbow lakes in the floodplain provide critical fish habitat needed
for feeding and rearing, leading researchers to conclude that the
entire floodplain should be considered a single functional unit,
essential to the river's biological integrity. Id. at 5-17 (citing
D.E. Shoup and D.H. Wahl, ``Fish Diversity and Abundance in Relation
to Interannual and Lake-Specific Variation in Abiotic
Characteristics of Floodplain Lakes of the Lower Kaskaskia River,
Illinois,'' Transactions of the American Fisheries Society 138:1076-
1092 (2009)). Since adjacent ponds are structurally and biologically
similar to oxbow lakes they serve similar functions relative to the
nearby river or stream. Waters, including wetlands, in the riparian
areas also provide food sources for stream invertebrates, which
colonize during inundation events. Id. at 5-19 (citing W.J. Junk, et
al., ``The Flood Pulse Concept in River-Floodplain Systems,'' in
D.P. Dodge, ed., Proceedings of the International Large River
Symposium Ottawa (Ottawa, Canada: Canadian Special Publication of
Fisheries and Aquatic Sciences 106, 1989), pp. 110-127; C. Ilg, et
al., ``Long-term Reactions of Plants and Macroinvertebrates to
Extreme Floods in Floodplain Grasslands,'' Ecology 89:2392-2398
(2008)). Riparian waters also form an integral part of the food web,
linking primary producers and plants to higher animals. Id. (citing
B. Malmqvist, ``Aquatic Invertebrates in Riverine Landscapes,''
Freshwater Biology 47:679-694 (2002); G.U.Y. Woodward and A.G.
Hildrew, ``Food Web Structure in Riverine Landscapes,'' Freshwater
Biology 47:777-798 (2002), T.K. Stead, et al., ``Secondary
Production of a Stream Metazoan Community: Does the Meiofauna Make a
Difference?,'' Limnology and Oceanography 50:398-403 (2005), D.J.
Woodford and A.R. McIntosh, ``Evidence of Source-Sink
Metapopulations in a Vulnerable Native Galaxiid Fish Driven by
Introduced Trout,'' Ecological Applications 20:967-977 (2010)).
Likewise, floodplains are important foraging, hunting, and breeding
sites for fish and amphibians. Id. at 5-15 (citing G.H. Copp, ``The
Habitat Diversity and Fish Reproductive Function of Floodplain
Ecosystems,'' Environmental Biology of Fishes 26:1-27 (1989); J.S.
Richardson, et al., ``Riparian Communities Associated with Pacific
Northwest Headwater Streams: Assemblages, Processes, and
Uniqueness,'' Journal of the American Water Resources Association
41:935-947 (2005)).
    Plants and animals move back and forth between riparian or
floodplain waters and the river network. This movement is assisted
in some cases when flooding events create hydrological connections.
For instance, these floodplain and riparian wetlands provide refuge,
feeding, and rearing habitat for many fish species. Id. at 5-17
(citing C.H. Wharton, et al., The Ecology of Bottomland Hardwood
Swamps of the Southeast: A Community Profile, FWS/OBS-81/37
(Washington, DC: U.S. Department of the Interior, Fish and Wildlife
Service, Biological Services Program, 1982); M.P. Matheney and C.F.
Rabeni, ``Patterns of Movement and Habitat Use by Northern
Hogsuckers in an Ozark Stream,'' Transactions of the American
Fisheries Society 124:886-897 (1995); A.A. Pease, et al., ``Habitat
and Resource Use by Larval and Juvenile Fishes in an Arid-Land River
(Rio Grande, New Mexico),'' Freshwater Biology 51:475-486 (2006);
J.A. Henning, et al., ``Use of Seasonal Freshwater Wetlands by
Fishes in a Temperate River Floodplain,'' Journal of Fish Biology
71:476-492 (2007); C.A. Jeffres, et al., ``Ephemeral Floodplain
Habitats Provide Best Growth Conditions for Juvenile Chinook Salmon
in a California River,'' Environmental Biology of Fishes 83:449-458
(2008)). Seeds ingested by animals such as carp are dispersed in
stream channels and associated waters. See, e.g., id. at 5-16
(citing B.J.A. Pollux, et al., ``Consequences of Intraspecific Seed-
Size Variation in Sparganium emersum for Dispersal by Fish,''
Functional Ecology 21:1084-1091 (2007)). Also, phytoplankton move
between floodplain wetlands and the river network. Id. at 5-17
(citing D.G. Angeler, et al., ``Phytoplankton community similarity
in a semiarid floodplain under contrasting hydrological connectivity
regimes,'' Ecological Research 25:513-520 (2010)). In turn, the
primary productivity conditions in the floodplain results in large
populations of phytoplankton that enrich river networks when
hydrological connections form. Id. (citing P.W. Lehman, et al.,
``The Influence of Floodplain Habitat on the Quantity and Quality of
Riverine Phytoplankton Carbon Produced During the Flood Season in
San Francisco Estuary,'' Aquatic Ecology 42:363-378 (2008)). This
influx of carbon into the river system nourishes the downstream
waters, for example, supporting fisheries.
    However, even when hydrological connections are absent, some
organisms can move between riparian waters and their neighboring
tributaries by overland movement in order to complete their life
cycle. River-dwelling mammals, such as river otters, move from the
river to riparian wetlands. Id. at 5-18 (citing D.G. Newman and C.R.
Griffin, ``Wetland Use by River Otters in Massachusetts,'' Journal
of Wildlife Management 58:18-23 (1994)). Several species of
amphibians and reptiles including frogs, snakes and turtles use both
streams and neighboring waters. Id. at 1-10, 5-4 to 5-5 (Table 5-1),
5-15 (citing J.S. Richardson, et al., ``Riparian Communities
Associated with Pacific Northwest Headwater Streams: Assemblages,
Processes, and Uniqueness,'' Journal of the American Water Resources
Association 41:935-947 (2005)). Movement between wetlands and the
river network also occurs by the dispersal of seed and plant
fragments and the wind dispersal of invertebrates. Id. at 5-15, 5-20
(citing R.L. Schneider and R.R. Sharitz, ``Hydrochory and
Regeneration in a Bald Cypress Water Tupelo Swamp Forest,'' Ecology
69:1055-1063 (1988); B. Middleton, ``Hydrochory, Seed Banks, and
Regeneration Dynamics Along the Landscape Boundaries of a Forested
Wetland,'' Plant Ecology 146:169-184 (2000); A.M. Gurnell,
``Analogies Between Mineral Sediment and Vegetative Particle
Dynamics in Fluvial Systems,'' Geomorphology 89:9-22 (2007); A.
Gurnell, et al., ``Propagule Deposition Along River Margins: Linking
Hydrology and Ecology,'' Journal of Ecology 96:553-565 (2008); C.
Nilsson, et al., ``The Role of Hydrochory in Structuring Riparian
and Wetland Vegetation,'' Biological Reviews 85:837-858 (2010); L.M.
Tronstad, et al., ``Aerial Colonization and Growth: Rapid
Invertebrate Responses to Temporary Aquatic Habitats in a River
Floodplain,'' Journal of the North American Benthological Society
26:460-471 (2007)). Animals, particularly migratory fish, may thus
move between adjacent waters and (a)(1) through (a)(3) waters. And
even when some species do not traverse the entire distance from
adjacent waters to downstream waters, the downstream waters still
benefit from the ecological integrity that persists because of the
close relationship that adjacent waters have with nearby waters.
This is because the chemical and biological properties that arise
from interactions between adjacent waters and tributaries move
downstream and support the integrity of (a)(1) through (a)(3)
waters.
    Biological connections between adjacent waters and river systems
do not always increase with hydrologic connections. In some cases,
the lack of connection improves the biological contribution provided
by riparian waters towards neighboring streams, rivers, and lakes.
For instance, the periodic hydrologic disconnectedness of oxbow
lakes is necessary for the accumulation of plankton, an important
source of carbon more easily assimilated by the aquatic food chain
than terrestrial forms of carbon. Id. at 5-46 (citing C. Baranyi, et
al., ``Zooplankton Biomass and Community Structure in a Danube River
Floodplain System: Effects of Hydrology,'' Freshwater Biology
47:473-482 (2002); S. Keckeis, et al., ``The Significance of
Zooplankton Grazing in a Floodplain System of the River Danube,''
Journal of Plankton Research 25:243-253 (2003)). Similarly, some
degree of hydrological disconnectedness is important in increasing
the number of mollusk species and macroinvertebrate diversity in
oxbow lakes, which in turn support the diversity of

mollusks throughout the aquatic system. Id. at 5-46 to 5-47 (citing
W. Reckendorfer, et al., ``Floodplain Restoration by Reinforcing
Hydrological Connectivity: Expected Effects on Aquatic Mollusc
Communities,'' Journal of Applied Ecology 43:474-484 (2006); K.
Obolewski, et al., ``Effect of Hydrological Connectivity on the
Molluscan Community Structure in Oxbow Lakes of the Lyna River,''
Oceanological and Hydrobiological Studies 38:75-88 (2009).

2. Confined Surface and Shallow Subsurface Hydrologic Connections
Significantly Affect the Chemical, Physical, or Biological Integrity of
(a)(1) Through (a)(3) Waters

    Wetlands and open waters, including those outside the riparian
zone and floodplain, can be connected downstream through
unidirectional flow from the wetland or open water to a nearby
tributary. Such connections can occur through a confined surface or
a shallow subsurface hydrologic connection. Report at 3-7, 5-23.
Outside of the riparian zone and floodplain, surface hydrologic
connections between adjacent waters and jurisdictional waters can
occur via confined flows (e.g. a swale, gully, ditch, or other
discrete feature). For purposes of this rule, confined surface
connections are defined as permanent, intermittent or ephemeral
surface connections through directional flowpaths, such as (but not
limited to) swales, gullies, rills, and ditches. In some cases,
these connections will be a result of ``fill and spill'' hydrology.
A directional flowpath is a path where water flows repeatedly from
the wetland or open water to the nearby jurisdictional water that at
times contains water originating in the wetland or open water as
opposed to just directly from precipitation. For the purposes of
this rule, ``fill and spill'' describes situations where wetlands or
open waters fill to capacity during intense precipitation events or
high cumulative precipitation over time and then spill to the
downstream jurisdictional water. Id. at 5-62 (citing T.C. Winter and
D.O. Rosenberry, ``Hydrology of Prairie Pothole Wetlands during
Drought and Deluge: A 17-year Study of the Cottonwood Lake Wetland
Complex in North Dakota in the Perspective of Longer Term Measured
and Proxy Hydrological Records,'' Climatic Change 40:189-209 (1998);
S.G. Leibowitz, and K.C. Vining, ``Temporal connectivity in a
prairie pothole complex,'' Wetlands 23:13-25 (2003)). Water
connected through such flows originate from the adjacent wetland or
open water, travel to the downstream jurisdictional water, and are
connected to those downstream waters by swales or other directional
flowpaths on the surface.
    A confined surface hydrologic connection, which may be
perennial, intermittent or ephemeral, supports periodic flows
between the adjacent water and the jurisdictional water. For
example, wetland seeps are likely to have perennial connections to
streams that provide important sources of baseflow, particularly
during summer. 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)). Other wetlands are connected to
streams via intermittent or ephemeral conveyances and can contribute
flow to downstream waters via their surface hydrologic connection.
Id. at 5-22 (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); B.P. Wilcox,
et al., ``Evidence of Surface Connectivity for Texas Gulf Coast
Depressional Wetlands,'' Wetlands 31:451-458 (2011)).The surface
hydrologic connection of the neighboring water to the jurisdictional
water and the close proximity of the waters enhance the neighboring
waters substantial effects the waters have on downstream (a)(1)
through (a)(3) waters. Wetlands and open waters that are connected
to (a)(1) through (a)(5) waters through a confined surface
hydrologic connection will have an impact on downstream (a)(1)
through (a)(3) waters, regardless of whether the outflow is
permanent, intermittent, or ephemeral. See, e.g., id. at 5-1 to 5-2.
    Wetlands and open waters with confined surface connections can
affect the physical integrity of waters to which they connect. Such
waters can provide an important source of baseflow to the streams to
which they are adjacent, helping to sustain the water levels in the
nearby streams. 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); 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); B.P. Wilcox,
et al., ``Evidence of Surface Connectivity for Texas Gulf Coast
Depressional Wetlands,'' Wetlands 31:451-458 (2011)) and T.M. Lee,
et al., Effect of Groundwater Levels and Headwater Wetlands on
Streamflow in the Charlie Creek Basin, Peace River Watershed, West-
Central Florida, U.S. Geological Survey Scientific Investigations
Report 2010-5189 (Reston, Virginia: U.S. Department of the Interior,
U.S. Geological Survey, 2010). Waters with a confined surface
connection to downstream jurisdictional waters can affect streamflow
by altering baseflow or stormflow through several mechanisms,
including surface storage and groundwater recharge. Report at 5-25.
Wetlands effectively store water because the entire aboveground
portion of the wetland basin is available for water storage, in
contrast to upland areas where soil particles or rock reduce water
storage volume for a given volume of that soil or rock (i.e., the
specific yield). Id. at 5-25 (citing A.I. Johnson, Specific Yield--
Compilation of Specific Yields for Various Materials, USGS Water
Supply Paper 1662-D (Washington, DC: U.S. Department of the
Interior, U.S. Geological Survey, 1967)). By storing water, these
waters can reduce peak streamflow, and thus, downstream flooding.
Id. at 5-25 (citing A. Bullock, and M. Acreman, ``The Role of
Wetlands in the Hydrological Cycle,'' Hydrology and Earth System
Sciences 7:358-389 (2003); P. McEachern, et al., ``Landscape Control
of Water Chemistry in Northern Boreal Streams of Alberta,'' Journal
of Hydrology 323:303-324 (2006)). Antecedent moisture conditions,
available wetland storage, and evaporation rates could impact water
storage, as some waters connected to jurisdictional waters via
discrete features may actually reduce flows in the streams they
neighbor during dry periods. Id. at 5-26 (citing A. Bullock, and M.
Acreman, ``The Role of Wetlands in the Hydrological Cycle,''
Hydrology and Earth System Sciences 7:358-389 (2003)). Thus,
wetlands and open waters with a confined hydrologic connection to
jurisdictional waters may function as a sink in dry periods if
storage capacity is not exceeded and evaporation rates surpass
groundwater recharge. Id. at 5-26 to 5-27.
    Wetlands and open waters with confined surface connections can
affect the chemical integrity of waters to which they connect. Such
waters can affect water quality of jurisdictional waters through
source and sink functions, often mediated by transformation of
chemical constituents. The surface hydrologic connections to nearby
jurisdictional waters provide pathways for materials transformed in
the wetlands and open waters (such as methylmercury or degraded
organic matter) to reach and affect the nearby waters and the
downstream (a)(1) through (a)(3). Id. at 5-27. Functions that occur
in the wetlands and open waters can affect downstream (a)(1) through
(a)(3) waters when compounds that are transformed in wetland
environments move to downstream waters via the surface hydrologic
connection. Id. at 5-28 (citing T.C. Winter and J.W. LaBaugh,
``Hydrologic Considerations in Defining Isolated Wetlands,''
Wetlands 23:532-540 (2003)). For example, methylmercury (which can
form in peatlands) can be transported through entrainment with
organic matter exports, and can move through surface flows from
peatlands with confined surface connections to downstream waters.
Id. at 5-28 (citing O. 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); V.L. St. Louis, et al., ``Importance of
Wetlands as Sources of Methyl mercury to Boreal Forest Ecosystems,''
Canadian Journal of Fisheries and Aquatic Sciences 51:1065-1076
(1994); 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);
P. Porvari, and M. Verta, ``Total and Methyl mercury Concentrations
and Fluxes from Small Boreal Forest Catchments in Finland,''
Environmental Pollution 123:181-191 (2003)). The mercury that is
transported downstream can enter the food chains of the

(a)(1) through (a)(3) waters and negatively impact wildlife
inhibiting those downstream waters. Id. at 5-28. Export of dissolved
organic matter from neighboring waters connected via a confined
surface connection can have potentially negative effects on
downstream waters because contaminants, such as MeHg and other trace
metals, can be adsorbed to the organic matter. Id. at 5-28 (citing
E.M. Thurman, Organic Geochemistry of Natural Waters (Boston, MA:
Martinus Nijhoff/Dr. W. Junk Publishers, 1985); 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)). Dissolved organic matter,
however, is also an important source of energy for downstream
aquatic communities. Id. at 5-28 (citing J.E. Hobbie and R.G.
Wetzel, ``Microbial control of dissolved organic carbon in lakes:
Research for the future,'' Hydrobiologia 229:169-180 (1992); K.R.
Reddy and R.D. DeLaune, Biogeochemistry of Wetlands: Science and
Applications, 774 p. (2008)). Wetlands with confined surface
hydrologic connections to the stream are connected to jurisdictional
tributary system and therefore can efficiently transport dissolved
organic carbon and other dissolved organic matter to the nearby
jurisdictional water and downstream (a)(1) through (a)(3) waters.
See, e.g., I.F. Creed, et al., ``Cryptic Wetlands: Integrating
Hidden Wetlands in Regression Models of the Export of Dissolved
Organic Carbon from Forested Landscapes,'' Hydrological Processes
17:3629-3648 (2003). Adjacent waters with a surface hydrologic
connection to jurisdictional waters can also improve water quality
through assimilation, transformation, or sequestration of nutrients
and other pollutants. Report at 5-29 (citing, e.g., K.R. Reddy, and
R.D. DeLaune, Biogeochemistry of Wetlands: Science and Applications,
774 p. (2008)). These processes can occur during times of lower
hydroperiods when water is not present in the surface hydrologic
connection between the adjacent water and the jurisdictional water.
Pollutants can be attenuated or retained in such adjacent waters
through processes including denitrification, ammonia volatilization,
microbial and plant biomass assimilation, sedimentation, sorption
and precipitation reactions, biological uptake, and long-term
storage in plant detritus. Id. at 5-29 (citing K.R. Reddy, et al.,
``Phosphorus Retention in Streams and Wetlands: A Review,'' Critical
Reviews in Environmental Science and Technology 29:83-146 (1999);
K.R. Reddy and R.D. DeLaune, Biogeochemistry of Wetlands: Science
and Applications, 774 p. (2008)). Through retention and mitigation
of pollutants and other chemical compounds, adjacent waters with a
surface hydrologic connection to jurisdictional waters can
substantially improve water quality downstream.
    Wetlands and open waters with confined surface connections can
affect the biological integrity of waters to which they connect.
Movement of organisms between these adjacent waters and the nearby
jurisdictional water is governed by many of the same factors that
affect movement of organisms between riparian/floodplain waters and
the river network. Id. at 5-31. Because such waters are at least
periodically hydrologically connected to the nearby jurisdictional
tributary network on the surface, dispersal of organisms can occur
actively through the surface connection or via wind dispersal,
hitchhiking, walking, crawling, or flying. See, e.g., id. at 5-31.
For example, waterborne dispersal of aquatic and emergent plants can
occur between the jurisdictional water and the neighboring water due
to the periodic hydrologic connection to the tributary system. Id.
at 5-31 (citing C. Nilsson, et al., ``The Role of Hydrochory in
Structuring Riparian and Wetland Vegetation,'' Biological Reviews
85:837-858 (2010)). Fish can also move between the jurisdictional
water and the neighboring water to which it is connected via a
surface hydrologic connection during periodic surficial hydrologic
connections. 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 and aquatic and semi-aquatic
amphibians and reptiles that can disperse overland can also
contribute to connectivity, as can aquatic birds, particularly given
the close proximity of the neighboring water to the jurisdictional
water. Mammals and birds can act as transport vectors for
hitchhikers like algae or aquatic insects. Id. at 5-32 (citing J.P.
Roscher, ``Alga Dispersal by Muskrat Intestinal Contents,''
Transactions of the American Microscopical Society 86:497-498
(1967)); 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)). Amphibians and reptiles move between
streams and their adjacent waters to satisfy part of their life-
history requirements. Id.at 5-33, Table 5-2. The hydrologic
connection between neighboring waters with a surface connection to
the jurisdictional water allows for that movement to occur either in
the water or over land. Aquatic insects that use both streams and
their adjacent waters can move outside of the stream network to the
nearby wetland or open water to seek suitable habitat for
overwintering, refuge from adverse conditions, hunting, foraging or
breeding, and then return to the stream for other life-history
requirements. 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 Freshwater
Invertebrates,'' Ecology Letters 6:783-796 (2003)). Neighboring
waters with a confined surface hydrologic connection to
jurisdictional waters help to maintain various biological
populations, which periodically replenish adjacent jurisdictional
waters, serving to maintain the biological integrity of (a)(1)
through (a)(3) waters.
    A shallow subsurface hydrologic connection is lateral water flow
through a shallow subsurface layer, such as can be found in steeply
sloping areas with shallow soils and soils with a restrictive
horizon that prevents vertical water flow, or in karst systems. K.J.
Devito, et al., ``Groundwater-Surface Water Interactions in
Headwater Forested Wetlands of the Canadian Shield,'' Journal of
Hydrology 181:127-47 (1996); M.A. O'Driscoll and R.R. Parizek, ``The
Hydrologic Catchment Area of a Chain of Karst Wetlands in Central
Pennsylvania, USA,'' Wetlands 23:171-79 (2003); B.J. Cook and F.R.
Hauer, ``Effects of Hydrologic Connectivity on Water Chemistry,
Soils, and Vegetation Structure and Function in an Intermontane
Depressional Wetland Landscape,'' Wetlands 27:719-38 (2007). Shallow
subsurface connections may be found below the ordinary root zone
(below 12 inches), where other wetland delineation factors may not
be present. The presence of an aquiclude (impervious layer) near the
surface leads to shallow subsurface flows through the soil, which
favors local groundwater flowpaths that connect to nearby wetlands
or streams. Report at 3-38.
    Wetlands with shallow subsurface connections can affect the
physical integrity of waters to which they connect. In general, the
volume and sustainability of streamflow within river networks
depends on contributions from groundwater, especially in areas with
shallow groundwater tables and pervious (meaning water can easily
pass through) subsurfaces. Id. at 3-12 (citing J.J. de Vries,
``Seasonal Expansion and Contraction of Stream Networks in Shallow
Groundwater Systems,'' Journal of Hydrology 170:15-26 (1995); T.C.
Winter, ``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 (2007); G.R. Kish, et
al., ``A Geochemical Mass-Balance Method for Base-Flow Separation,
Upper Hillsborough River Watershed, West-Central Florida, 2003-2005
and 2009,'' USGS Scientific Investigations Report 2010-5092
(Washington, DC: U.S. Department of the Interior, U.S. Geological
Survey, 2010). Because wetlands with shallow subsurface connections
to streams and rivers provide some of these groundwater
contributions, they influence the flow regime. Wetlands connected
via shallow subsurface connections also can act as water sinks when
evapotranspiration is high, but as water sources when
evapotranspiration is low. Id.

at 3-25. As a result, these adjacent waters moderate peak flows,
reduce downstream flooding, and provide runoff to help maintain
baseflow for streams during times of low flows.
    Wetlands and other waters with shallow subsurface connections
affect the chemical and biological integrity of downstream waters in
ways similar to wetlands with surface connections. The distance
between these wetlands and jurisdictional waters may influence the
connectivity since wetlands with shorter distances to the stream
network will have higher hydrological and biological connectivity
than wetlands located further from the same network. Id. at 3-43.
The distance between the wetland and water may also influence
whether waters are connected via surface or shallow subsurface
hydrologic connections, as wetlands and open waters that are closer
to rivers and streams will have a higher probability of being
connected than more distant waters, assuming that conditions
governing type and quantity of flows (e.g. slope, soil and aquifer
permeability) are similar. Id at 5-2. For wetlands connected to
tributaries through groundwater flows, less distant wetlands/waters
are generally connected through shallower flowpaths, assuming
similar soil and geologic properties. Id. at 3-11 (Figure 3-5), 3-
42. These shallower subsurface flows have the greatest interchange
with surface waters and travel between points in the shortest amount
of time. Id. at 3-42.

3. Adjacent Waters, Including Wetlands, Separated From Other ``Waters
of the United States'' by Man-Made Dikes or Barriers, Natural River
Berms, Beach Dunes and the Like Significantly Affect the Chemical,
Physical, or Biological Integrity of (a)(1) Through (a)(3) Waters

    The terms earthen dam, dike, berm, and levee are used to
describe similar structures whose primary purpose is to help control
flood waters. Such structures vary in scale and size. A levee is an
embankment whose primary purpose is to furnish flood protection from
seasonal high water and which is therefore subject to water loading
for periods of only a few days or weeks a year. Earthen embankments
that are subject to water loading for prolonged periods (longer than
normal flood protection requirements) are called earth dams. There
are a wide variety of types of structures and an even wider set of
construction methods. These range from a poorly constructed, low
earthen berm pushed up by a backhoe to a well-constructed,
impervious core, riprap lined levee that protects houses and
cropland. Generally, levees are built to detach the floodplain from
the channel, decreasing overbank flood events. S.B. Franklin, et
al., ``Complex Effects of Channelization and Levee Construction on
Western Tennessee Floodplain Forest Function,'' Wetlands 29(2): 451-
464 (2009). The investigation methods to determine the presence or
absence of the hydrologic connection depend on the type of
structure, the underlying soils, the presence of groundwater, and
the depth of the water table. Department of the Army, U.S. Army
Corps of Engineers, Engineering and Design--Design and Construction
of Levees, EM 1110-2-1913 (Washington, DC, Department of the Army,
2000), p. 1-1.
    Man-made berms and the like are fairly common along streams and
rivers across the United States and often accompany stream
channelization. S.B. Franklin, et al., ``Complex Effects of
Channelization and Levee Construction on Western Tennessee
Floodplain Forest Function,'' Wetlands 29(2): 451-464 (2009). One
study conducted in Portland, Oregon found that 42% of surveyed
wetlands had dams, dikes, or berms. M. Kentula, et al., ``Tracking
Changes in Wetlands with Urbanization: Sixteen Years of Experience
in Portland, Oregon, USA,'' Wetlands 24(4):734-743 (2004). Likewise,
over 90% of the tidal freshwater wetlands of the Sacramento-San
Joaquin Delta have been diked or leveed. C. Simenstad, et al.,
``Preliminary Results from the Sacramento-San Joaquin Delta Breached
Levee Wetland Study,'' Interagency Ecological Program for the
Sacramento-San Joaquin Estuary Newsletter 12(4):15-21 (1999). At
least 40,000 kilometers of levees, floodwalls, embankments, and
dikes are estimated across the United States, with approximately
17,000 kilometers of levees in the Upper Mississippi Valley alone.
SE. Gergel, et al., ``Consequences of Human-altered Floods: Levees,
Floods, and Floodplain Forests along the Wisconsin River,''
Ecological Applications 12(6): 1755-1770 (2002).
    Adjacent waters separated from the tributary network by dikes,
levees, berms and the like continue to have a hydrologic connection
to downstream waters. This is because berms and similar features
typically do not block all water flow. Indeed, even dams, which are
specifically designed and constructed to impound large amounts of
water effectively and safely, do not prevent all water flow, but
rather allow seepage under the foundation of the dam and through the
dam itself. See, e.g., International Atomic Energy Agency, Factsheet
on Investigating Leaks through Dams and Reservoirs, http://www.tc.iaea.org/tcweb/publications/factsheets/sheet20dr.pdf; U.S.
Bureau of Reclamation, Provo Office, Safety of Dams, http://www.usbr.gov/uc/provo/progact/damsafety.html; Federal Energy
Regulatory Commission (FERC), ``Chapter 14: Dam Safety Performance
Monitoring Program,'' Engineering Guidelines for the Evaluation of
Hydropower Projects (FERC, 2005), pp. 14-36 to 14-39.
    Seepage is the flow of a fluid through the soil pores. Seepage
through a dam, through the embankments, foundations or abutments, or
through a berm is a normal condition. D.A. Kovacic, et al.,
``Effectiveness of Constructed Wetlands in Reducing Nitrogen and
Phosphorus Export from Agricultural Tile Drainage,'' Journal of
Environmental Quality 29(4): 1262-1274 (2000); Federal Energy
Regulatory Commission (FERC), ``Chapter 14: Dam Safety Performance
Monitoring Program,'' Engineering Guidelines for the Evaluation of
Hydropower Projects (FERC, 2005), pp. 14-36 to 14-39. This is
because water seeks paths of least resistance through the berm or
dam and its foundation. Michigan Department of Environmental
Quality, Seepage Through Earth Dams (2002), http://www.michigan.gov/deq/0,1607,7-135-3313_3684_3723-9515-,00.html. All earth and rock-
fill dams are subject to seepage through the embankment, foundation,
and abutments. Department of the Army, U.S. Army Corps of Engineers,
Seepage Analysis and Control for Dams, EM 1110-2-1901, (Washington,
DC: Department of the Army, Original 1986--Revised 1993), Page 1-1;
Department of the Army, U.S. Army Corps of Engineers, Engineering
and Design: General Design and Construction Considerations for Earth
and Rock-filled Dams, EM 1110-2-2300 (Washington, DC: Department of
the Army, 2004), pp. 6-1 to 6-7. Concrete gravity and arch dams
similarly are subject to seepage through the foundation and
abutments. Department of the Army, U.S. Army Corps of Engineers,
Seepage Analysis and Control for Dams, EM 1110-2-1901 (Washington,
DC: Department of the Army, Original 1986--Revised 1993), Page 1-1.
Levees and the like are subject to breaches and breaks during times
of floods. C. Nilsson, et al., ``Fragmentation and Flow Regulation
of the World's Large River Systems,'' Science 308(5720):405-408
(2005). Levees are similarly subject to failure in the case of
extreme events, such as the extensive levee failures caused by
Hurricanes Katrina and Rita. J.W. Day, et al., ``Restoration of the
Mississippi Delta: Lessons from Hurricanes Katrina and Rita,''
Science 315(5819): 1679-1684 (2007). In designing levees and similar
structures, seepage control is necessary to prevent possible failure
caused by excessive uplift pressures, instability of the downstream
slope, piping through the embankment and/or foundation, and erosion
of material by migration into open joints in the foundation and
abutments. Id.; D.A. Kovacic, et al., ``Effectiveness of Constructed
Wetlands in Reducing Nitrogen and Phosphorus Export from
Agricultural Tile Drainage,'' Journal of Environmental Quality
29(4): 1262-1274 (2000); U.S. Department of the Interior, Bureau of
Reclamation, Upper Colorado Region, see http://www.usbr.gov/uc/provo/progact/damsafety.html; International Atomic Energy Agency,
Investigating Leaks through Dams and Reservoirs, see  http://www-tc.iaea.org/tcweb/publications/factsheets/sheet20dr.pdf; California
Division of Safety of Dams, Embankment Design, see http://damsafety.water.ca.gov/guidelines/embankment.htm.
    The rate at which water moves through the embankment depends on
the type of soil in the embankment, how well it is compacted, the
foundation and abutment preparation, and the number and size of
cracks and voids within the embankment. All but the smallest earthen
dams are commonly built with internal subsurface drains to intercept
water seeping from the reservoir (i.e., upstream side) to the
downstream side. Department of the Army, U.S. Army Corps of
Engineers, Construction Control for Earth and Rock-filled Dams, EM
1110-2-1911, September 30, 1995, Washington, DC 20314-1000, Page 1-
1. Where it is not intercepted by a subsurface drain, the seepage
will emerge downstream from or at the toe of the embankment.
Michigan Department of Environmental Quality, Seepage Through Earth
Dams (2002), http://www.michigan.gov/deq/0,1607,7-135-

3313--3684--3723-9515-,00.html. Seepage may vary in appearance from
a ``soft,'' wet area to a flowing ``spring.'' It may show up first
as an area where the vegetation is lush and darker green. Cattails,
reeds, mosses, and other marsh vegetation may grow in a seepage
area. Michigan Department of Environmental Quality, Seepage Through
Earth Dams (2002), http://www.michigan.gov/deq/0,1607,7-135-3313_3684_3723-9515-,00.html.
    Engineered berms are typically designed to interfere with the
seasonal pattern of water level (hydroperiod) of the area behind the
berm, reducing the frequency and severity of inundation. Berms are
not designed to eliminate all hydrologic connection between the
channel on one side and the area behind the berm on the other. It is
almost always impracticable to build a berm that will not be
overtopped by a flood of maximum severity, and most berms are not
designed to withstand severe floods. See, e.g., Department of the
Army, U.S. Army Corps of Engineers, Seepage Analysis and Control for
Dams, EM 1110-2-1901, (Washington, DC: Department of the Army,
Original 1986--Revised 1993), Page 1-1. Levees are designed to allow
seepage and are frequently situated on foundations having natural
covers of relatively fine-grain impervious to semipervious soils
overlying pervious sands and gravels. Department of the Army, U.S.
Army Corps of Engineers, Engineering and Design: Design Guidance for
Levee Underseepage, ELT 1110-2-569, Washington, DC: Department of
the Army, 2005), pp. 1-9. These surface strata constitute impervious
or semipervious blankets when considered in connection with seepage.
Principal seepage control measures for foundation underseepage are
(a) cutoff trenches, (b) riverside impervious blankets, (c)
landslide berms, (d) pervious toe trenches, and (e) pressure relief
wells. Department of the Army, U.S. Army Corps of Engineers,
Engineering and Design--Design and Construction of Levees, EM 1110-
2-1913 (Washington, DC, Department of the Army, 2000), p. 1-1.
Overtopping of an embankment dam is very undesirable because the
embankment materials may be eroded away. Additionally, only a small
number of concrete dams have been designed to be overtopped. Water
normally passes through the main spillway or outlet works; it should
pass over an auxiliary spillway only during periods of high
reservoir levels and high water inflow. All embankment and most
concrete dams have some seepage. See, e.g., http://www.damsafety.org/layout/subsection.aspx?groupid=14&contentid=47.
However, it is important to control the seepage to prevent internal
erosion and instability. Proper dam construction, and maintenance
and monitoring of seepage provide control.
    Berm-like landforms known as natural levees occur naturally and
do not isolate adjacent wetlands from the streams that form them.
Natural levees and the wetlands and waters behind them are part of
the floodplain, including along some small streams and streams in
the Arid West. C.A. Johnston, et al., ``Nutrient Dynamics in
Relation to Geomorphology of Riverine Wetlands,'' Soil Science
Society of America Journal 65(2):557-577 (2001). Every flowing
watercourse transports not only water, but sediment--eroding and
rebuilding its banks and floodplains continually. Federal
Interagency Stream Restoration Working Group, Stream Corridor
Restoration: Principles, Processes and Practices, USDA National
Engineering Handbook Part 653 (1999). Different deposition patterns
occur under varying levels of streamflow, with higher flows having
the most influence on the resulting shape of streambanks and
floodplains. Id. In relatively flat landscapes drained by low-
gradient streams, this natural process deposits the most sediment on
the bank immediately next to the stream channel while floodplains
farther from the channel are usually lower-lying wetlands
(``backswamps'' or ``backwater wetlands'') that receive less
sediment. See, e.g., C.A. Johnston, et al., ``The Potential Role of
Riverine Wetlands as Buffer Zones,'' in N.E. Haycock, et al., ed.,
Buffer Zones Their Processes and Potential in Water Protection
(Quest International, 1997), pp. 155-170. The somewhat elevated land
thus built up at streamside is called a natural levee, and this
entirely natural landform is physically and hydrologically similar
to narrow, man-made berms. See, e.g., L.B. Leopold, et al., Fluvial
Processes in Geomorphology (Toronto: General Publishing Co. Ltd.,
1964). Natural levees are discontinuous, which allows for a
hydrologic connection to the stream or river via openings in the
levees and thus the periodic mixing of river water and backwater.
C.A. Johnston, et al., ``Nutrient Dynamics in Relation to
Geomorphology of Riverine Wetlands,'' Soil Science Society of
America Journal 65(2): 557-577 (2001). In addition, streams with
natural levees, in settings with no human interference whatsoever,
retain hydrologic connection with their wetlands behind the levees
by periodic flooding during high water and via seepage through and
under the levee. Similarly, man-made berms are typically
periodically overtopped with water from the near-by stream, and as
previously mentioned, are connected via seepage.
    Waters, including wetlands, separated from a stream by a natural
or man-made berm serve many of the same functions as those discussed
above on other adjacent waters. Furthermore, even in cases where a
hydrologic connection may not exist, there are other important
considerations, such as chemical and biological factors, that result
in a significant nexus between the adjacent wetlands or waters and
the nearby ``waters of the United States,'' and (a)(1) through
(a)(3) waters.
    The movement of surface and subsurface both over berms and
through soils and berms adjacent to rivers and streams is a
hydrologic connection between wetlands and flowing watercourses. The
intermittent connection of surface waters over top of, or around,
natural and manmade berms further strengthens the evidence of
hydrologic connection between wetlands and flowing watercourses.
Both natural and man-made barriers can be topped by occasional
floods or storm events. See, e.g., R.E. Turner, et al., ``Wetland
Sedimentation from Hurricanes Katrina and Rita,'' Science 314(5798):
449-452 (2006); P.A. Keddy, et al., ``The Wetlands of Lakes
Pontchartrain and Maurepas: Past, Present and Future,''
Environmental Reviews 15: 43-77 (2007). When berms are periodically
overtopped by water, wetlands and waters behind the barriers are
directly connected to and interacting with the nearby stream and its
downstream waters. In addition, surface waters move to and from
adjacent soils (including adjacent wetland soils) continually. Along
their entire length, streams alternate between effluent (water-
gaining) and influent (water-losing) zones as the direction of water
exchange with the streambed and banks varies. Federal Interagency
Stream Restoration Working Group, Stream Corridor Restoration:
Principles, Processes and Practices, USDA National Engineering
Handbook Part 653 (1999). The adjacent areas involved in this
surface water exchange with a stream or river are known as the
hyporheic zone. Hyporheic zone waters are part of total surface
waters temporarily moving through soil or sediment. Like within-
channel waters, these waters are oxygenated and support living
communities of organisms in the hyporheic zone.
    Because a hydrologic connection between adjacent wetlands and
waters and downstream waters still exists despite the presence of a
berm or the like, the chemical and biological connections that rely
on a hydrologic connection also exist. For instance, adjacent waters
behind berms can still serve important water quality functions,
serving to filter pollutants and sediment before they reach
downstream waters. Wetlands behind berms can function to filter
pollutants before they enter the nearby tributary, with the water
slowly released to the stream through seepage or other hydrological
connections. See, e.g., L.L. Osborne and D.A. Kovacic, ``Riparian
Vegetated Buffer Strips in Water-Quality Restoration and Stream
Management,'' Freshwater Biology 29(2): 243-258 (1993); D.A.
Kovacic, et al., ``Effectiveness of Constructed Wetlands in Reducing
Nitrogen and Phosphorus Export from Agricultural Tile Drainage,''
Journal of Environmental Quality 29(4): 1262-1274 (2000). Their
ability to retain sediment and floodwaters may be enhanced by the
presence of the berm. For instance, some backwater wetlands in
floodplain/riparian areas exhibit higher sedimentation rates than
streamside locations. E.J. Kuenzler, et al., ``Distributions and
Budgets of Carbon, Phosphorus, Iron and Manganese in a Floodplain
Swamp Ecosystem,'' Water Resources Research Institute Report 157
(Chapel Hill, NC: University of North Carolina, 1980); C.A.
Johnston, et al., ``Nutrient Dynamics in Relation to Geomorphology
of Riverine Wetlands,'' Soil Science Society of America Journal
65(2): 557-577 (2001). The presence of manmade levees can actually
increase denitrification rates, meaning that the adjacent waters can
more quickly transform nitrogen. SE. Gergel, et al., ``Do Dams and
Levees Impact Nitrogen Cycling? Simulating the Effects of Flood
Alterations on Floodplain Denitrification,'' Global Change Biology
11(8): 1352-1367 (2005). However, the presence of manmade berms does
limit

the ability of the river to connect with its adjacent wetlands
through overbank flooding and thus limits sediment, water and
nutrients transported from the river to the adjacent waters. Id.;
J.L. Florsheim and J.F. Mount, ``Changes in Lowland Floodplain
Sedimentation Processes: Pre-disturbance to Post-rehabilitation,
Cosumnes River, CA,'' Geomorphology 56(3-4):305-323 (2003). However,
the presence of a berm does not completely eliminate the transport
of sediments and water from the river to the nearby adjacent
wetland, as suspended sediments and water can overflow both natural
and man-made levees, though the transport is usually more pronounced
in settings with natural levees. See, e.g., R.E. Turner, et al.,
``Wetland Sedimentation from Hurricanes Katrina and Rita,'' Science
314(5798):449-452 (2006); P.A. Keddy, et al., ``The Wetlands of
Lakes Pontchartrain and Maurepas: Past, Present and Future,''
Environmental Reviews 15:43-77 (2007). Sediment deposition over
levees is particularly enhanced by extreme events like hurricanes.
Id.; D.J. Reed, et al., ``Reducing the Effects of Dredged Material
Levees on Coastal Marsh Function: Sediment Deposition and Nekton
Utilization,'' Environmental Management 37(5):671-685 (2006).
Wetlands behind berms, where the system is extensive, can help
reduce the impacts of storm surges caused by hurricanes. J.W. Day,
et al., ``Restoration of the Mississippi Delta: Lessons from
Hurricanes Katrina and Rita,'' Science 315(5819):1679-1684 (2007).
    Adjacent waters, including wetlands, separated from water bodies
by berms and the like maintain ecological connection with those
water bodies. Though a berm may reduce habitat functional value and
may prevent some species from moving back and forth from the wetland
to the river, many major species that prefer habitats at the
interface of wetland and stream ecosystems remain able to utilize
both habitats despite the presence of such a berm. Additional
species that are physically isolated in either stream or wetlands
habitat still interact ecologically with species from the other
component. Thus, adjacent wetlands with or without small berms can
retain numerous similarities in ecological function. For example:
Wetland bird species such as wading birds are able to utilize both
wetland and adjacent stream/ditch habitats; wetland amphibians would
be able to bypass the berm in their adult stage; aquatic
invertebrates and fish would still interact with terrestrial/wetland
predators and prey in common food web relationships despite the
presence of a berm. See, e.g., G.S. Butcher, and B. Zimpel,
``Habitat Value of Isolated Waters to Migratory Birds,'' Prepared by
Cornell Laboratory of Ornithology and The Cadmus Group, Inc. for
U.S. Environmental Protection Agency Office of Wetlands Protection,
(Washington, DC: Cornell and Cadmus, 1991); M.F. Willson and K.C.
Halupka, ``Anadromous Fish as Keystone Species in Vertebrate
Communities,'' Conservation Biology 9(3):489-497 (1995); C.J.
Cederholm, et al., ``Pacific Salmon Carcasses: Essential
Contributions of Nutrients and Energy for Aquatic and Terrestrial
Ecosystems,'' Fisheries 24(10):6-15 (1999); S.S. Schwartz and D.G.
Jenkins, ``Temporary Aquatic Habitats: Constraints and
Opportunities,'' Aquatic Ecology 34:3-8 (2000); D.T. Bilton, et al.,
``Dispersal in Freshwater Invertebrates,'' Annual Review of Ecology
and Systematics 32:159-81 (2001).
    One example of adjacent waters behind berms and the like are
interdunal wetlands located in coastal areas, including some areas
of the Great Lakes and along barrier islands. Interdunal wetlands
form in swales or depressions within open dunes or between beach
ridges along the coast and experience a fluctuating water table
seasonally and yearly in synchrony with sea or lake level changes.
W.E. Odum, ``Non-Tidal Freshwater Wetlands in Virginia,'' Virginia
Journal of Natural Resources Law 7: 421-434 (1988); D.A. Albert,
Borne of the Wind: An Introduction to the Ecology of Michigan Sand
Dunes (Lansing, MI: Michigan Natural Features Inventory, 2000), 63
pp.; D.A. Albert, Between Land and Lake: Michigan's Great Lakes
Coastal Wetlands, Bulletin E-2902 (East Lansing, MI: Michigan
Natural Features Inventory, Michigan State University Extension,
2003), 96 pp; D.A. Albert, Natural Community Abstract for Interdunal
Wetland (Lansing, MI: Michigan Natural Features Inventory, 2007), 6
pp. For those along the ocean coast, they are typically formed as a
result of oceanic processes where the wetlands establish behind
relict dune ridges (dunes that were formed along a previously
existing coast line). Wetlands in the interdunal system are in close
proximity to each other and to the surrounding (a)(1) through (a)(3)
waters. Their proximity to one another and to the (a)(1) through
(a)(3) waters indicates a close physical relationship between
interdunal wetland systems and the traditional navigable waters,
interstate waters, or the territorial seas. Despite the presence of
the beach dunes, interdunal wetlands have chemical, physical, or
biological connections that greatly influence the integrity of the
nearby (a)(1) through (a)(3) waters. The wetlands are hydrologically
connected to these (a)(1) through (a)(3) waters through unconfined,
directional flow and shallow subsurface flow during normal
precipitation events and extreme events. As previously noted, they
are linked to the rise and fall of the surrounding tides--the water-
level fluctuations of the nearby (a)(1) through (a)(3) waters are
important for the dynamics of the wetlands. D.A. Albert, Between
Land and Lake: Michigan's Great Lakes Coastal Wetlands, Bulletin E-
2902 (East Lansing, MI: Michigan Natural Features Inventory,
Michigan State University Extension, 2003), 96 pp. The wetlands
provide floodwater storage and attenuation, retaining and slowly
releasing floodwaters before they reach the nearby (a)(1) through
(a)(3) waters. Like other adjacent wetlands, interdunal wetlands
also have important chemical connections to the nearby (a)(1)
through (a)(3) waters, as they serve important water quality
benefits. The wetlands store sediment and pollutants that would
otherwise reach the surrounding (a)(1) through (a)(3) waters. The
wetlands are biologically connected to the surrounding (a)(1)
through (a)(3) waters. For instance, they provide critical habitats
for species that utilize both the wetlands and the nearby (a)(1)
through (a)(3) waters, supporting high diversity and structure.
Habitat uses include basic food, shelter, and reproductive
requirements. Aquatic insects, amphibians, and resident and
migratory birds all use interdunal wetlands as critical habitat, and
the wetlands provide better shelter than the nearby exposed beach.
D.A. Albert, Borne of the Wind: An Introduction to the Ecology of
Michigan Sand Dunes (Lansing, MI: Michigan Natural Features
Inventory, 2000), 63 pp.; S.M. Smith, et al., ``Development of
Vegetation in Dune Slack Wetlands of Cape Cod National Seashore
(Massachusetts, USA),'' Plant Ecology 194(2): 243-256 (2008). In
marine coastal areas, the wetlands are often the only freshwater
system in the immediate landscape, thus providing critical drinking
water for the species that utilize both the wetlands and the nearby
(a)(1) through (a)(3) waters, although some interdunal wetlands are
brackish in nature. See, e.g., C.M. Heckscher and C.R. Bartlett,
``Rediscovery and Habitat Associations of Photuris Bethaniensis
McDermott (Coleoptera: Lampyridae),'' The Coleopterists Bulletin
58(3): 349-353 (2004).
    Wetlands behind the extensive levee system in the Yazoo Basin
are an example of adjacent waters behind man-made barriers. A
regional hydrogeomorphic approach guidebook for the Yazoo Basin of
the Lower Mississippi River Alluvial Valley assesses the functions
of these wetlands. R.D. Smith and C.V. Klimas, A Regional Guidebook
for Applying the Hydrogeomorphic Approach to Assessing Wetland
Functions of Selected Regional Wetland Subclasses, Yazoo Basin,
Lower Mississippi River Alluvial Valle, Prepared for the U.S. Army
Corps of Engineers, ERDC/EL TR-02-4 (2002). An extensive levee
system was built along the river system to prevent flooding of the
Mississippi River, resulting in drastic effects to the hydrology of
the basin. Id. at 47. Despite the alteration of hydrology in the
basin, extensive wetlands systems still exist behind the man-made
and natural levees and maintain a hydrologic connection to the river
system. These wetlands detain floodwater, detain precipitation,
cycle nutrients, export organic carbon, remove elements and
compounds, maintain plant communities, and provide fish and wildlife
habitat. Id. The functions in turn provide numerous and substantial
benefits to the nearby river.

4. Conclusions Regarding Adjacent Waters

    The scientific literature documents that waters which are
adjacent to (a)(1) through (a)(5) waters, including wetlands, oxbow
lakes and adjacent ponds, are integral parts of tributary networks
to (a)(1) through (a)(3) waters because they are directly connected
to streams via permanent surface features that concentrate, mix,
transform, and transport water and other materials, including food
resources, downstream to larger rivers. Adjacent wetlands and other
adjacent waters filter pollutants before they enter the tributary
system, they attenuate flow during flood events, they regulate flow
rate and timing, they trap sediment, and they input organic material
into rivers and streams, providing the basic building blocks for
their

healthy functioning. These waters also are biologically connected to
downstream waters by providing habitat and refuge to many species,
and storing and releasing food sources. The scientific literature
demonstrates that adjacent waters in a watershed together exert a
strong influence on the character and functioning of rivers, streams
and lakes.
    Adjacent waters, as defined, alone or in combination with other
adjacent waters in a watershed, significantly affect the chemical,
physical, or biological integrity of traditional navigable waters,
interstate waters, and the territorial seas. Based on studies of
waters in riparian areas, flood plains, and their hydrologic
connections through the tributary system there is sufficient
scientific evidence regarding the important functions of these
adjacent wetlands to demonstrate that, alone or in combination with
similarly situated waters in the region, wetlands and open waters
adjacent to any tributary have a significant effect on the chemical,
physical, or biological integrity of traditional navigable waters,
interstate waters, or the territorial seas. The reviewed scientific
literature supports the conclusion that adjacent waters generally
play a larger role in the ecological condition of smaller tributary
systems, which, in turn, determines the effects on the chemical,
physical, and biological health of larger downstream waters.

iii. ``Other Waters''

    The Report includes a focused evaluation of the connections and
effects to downstream waters for several regional types of streams
and wetlands: Prairie streams, southwest intermittent and ephemeral
streams, oxbow lakes, Carolina and Delmarva bays, prairie potholes,
and vernal pools. These regional types were chosen for evaluation
because they represent a broad geographic area as well as a
diversity of water types based on their origin, landscape setting,
hydrology, and other factors. Most prairie streams and southwest
intermittent and ephemeral streams are likely to be considered
tributaries to (a)(1) through (a)(3) waters (with the exception of
streams, for example, located in closed basins, which lack an (a)(1)
through (a)(3) water or a connection thereto); similarly, most oxbow
lakes are likely to be considered adjacent to (a)(1) through (a)(5)
waters. Carolina and Delmarva bays, prairie potholes, and vernal
pools may or may not be considered adjacent to (a)(1) through (a)(5)
waters. Where waters are not considered tributaries (e.g. waters in
a solely intrastate closed basin that does not contain a traditional
navigable water, interstate water, or a territorial sea, or a
connection thereto) or where waters, including wetlands, do not meet
the proposed regulatory definition of adjacent, they should be
evaluated to determine whether they are (a)(7) waters. The agencies
seek comment on establishing such categories, as well as on other
options for addressing ``other waters.''
    The term ``other waters'' refers to waters that cannot be
considered ``adjacent'' to downstream jurisdictional waters and that
are not tributaries of such waters. ``Other waters'' are found
outside the riparian zone and the floodplain, as waters within these
areas are considered to be ``adjacent.'' As such, wetlands that are
``other waters'' typically will have unidirectional flow. As
mentioned in Part II, section 2.B. above, many unidirectional
wetlands are considered adjacent and interact with downstream
jurisdictional waters through channels, shallow subsurface flow, or
by providing additional functions such as storage and mitigating
peak flows. Unidirectional wetlands that lack a confined surface
connection or a shallow subsurface connection to downstream waters
and are surrounded by uplands will typically fall under the
definition of ``other waters,'' and are often referred to in
scientific literature and policy as ``geographically isolated
waters.'' The term ``geographically isolated'' should not be used to
implicate the lack of connectivity to downstream waters, as these
wetlands are often connected to downstream waters through deeper
groundwater connections, biological connections, or spillage. The
degree of connectivity of such wetlands will vary depending on
landscape features such as distance from downstream waters and
proximity to other wetlands of similar nature that as a group
connect to jurisdictional downstream waters. Report at 3-43, 5-2.
    For purposes of assessing whether a particular water is a
``water of the United States'' because it, alone or in combination
with other similarly situated waters, has a significant nexus to an
(a)(1) through (a)(3) water, the agencies are proposing to define
each of the elements of Justice Kennedy's significant nexus standard
in the definition of ``significant nexus.''

A. In the Region

    The agencies have determined that because the movement of water
from watershed drainage basins to river networks and lakes shapes
the development and function of these systems in a way that is
critical to their long term health, the watershed is a reasonable
and technically appropriate interpretation of Justice Kennedy's
standard. See, e.g., D.R. Montgomery, ``Process Domains and the
River Continuum,'' Journal of the American Water Resources
Association 35:397-410 (1999).
    Using a watershed as the framework for conducting significant
nexus evaluations is scientifically supportable. Watersheds are
generally regarded as the most appropriate spatial unit for water
resource management. See, e.g., J.M. Omernik and R.G. Bailey,
``Distinguishing Between Watersheds and Ecoregions,'' Journal of the
American Water Resources Association 33.5: 939-40 (1997); D.R.
Montgomery, ``Process Domains and the River Continuum,'' Journal of
the American Water Resources Association 35: 397-410 (1999); T.C.
Winter ``The Concept of Hydrologic Landscapes,'' Journal of the
American Water Resources Association 37: 335-49 (2001); J.S. Baron,
et al., ``Meeting Ecological and Societal Needs for Freshwater,''
Ecological Applications 12: 1247-60 (2002); J.D. Allan, ``Landscapes
and Riverscapes: The Influence of Land Use on Stream Ecosystems,''
Annual Review of Ecology Evolution and Systematics 35: 257-84
(2004); United States, EPA 841-B-08-002: U.S. Environmental
Protection Agency, Handbook for Developing Watershed Plans to
Restore and Protect Our Waters: Planning & Implementation Steps
(Washington D.C.: U.S. EPA, March 2008); P.J. Wigington, et al.,
``Oregon Hydrologic Landscapes: A Classification Framework,''
Journal of the American Water Resources Association 49.1:163-82
(2013). Anthropogenic actions and natural events can have widespread
effects within the watershed that collectively impact the quality of
the relevant traditional navigable water, interstate water or
territorial sea. 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, D.C.: U.S. EPA and USDA/ARS Southwest Watershed
Research Center, Levick et al., 2008) (Levick, et. al.). For these
reasons, it is more appropriate to conduct a significant nexus
determination at the watershed scale than to focus on a specific
site, such as an individual stream segment. The watershed size
reflects the specific water management objective, and is scaled up
or down as is appropriate to meet that objective. If the objective
is to manage the water quality in a particular receiving water body
(the ``target'' water body), the watershed should include all those
waters that are contributing to that target water since they will
primarily determine the quality of the receiving water.
    The watershed that drains to the single point of entry to a
traditional navigable water, interstate water or territorial sea is
a logical spatial framework for the evaluation of the nexus. This is
because, from a water quality management perspective, the (a)(1),
(a)(2) or (a)(3) water is the downstream affected water whose
quality is dependent on the condition of the contributing upstream
waters, including streams, lakes, and wetlands. To restore or
maintain the health of the downstream affected water, it is standard
practice to evaluate the condition of the waters that are in the
contributing watersheds and to develop a plan to address the issues
of concern. The functions of the contributing waters are
inextricably linked and have a cumulative effect on the integrity of
the downstream traditional navigable water, interstate water or
territorial sea. The size of that watershed can be determined by
identifying the geographic area that drains to the nearest
traditional navigable water, interstate water or the territorial
seas, and then using that point of entry watershed to conduct a
significant nexus evaluation. P.E. Black, ``Watershed Functions,''
Journal of the American Water Resources Association 33.1:1-11
(1997).
    The Corps is organized based on watersheds and has used
watershed framework approaches for water sources, navigation
approaches for over 100 years, and in the regulatory program since
its inception. Also, using a watershed framework is consistent with
over two decades of practice by EPA and many other governmental,
academic, and other entities which recognize that a watershed
approach is the most effective framework to address water resource
challenges. U.S. Environmental Protection Agency, The

Watershed Protection Approach Framework (Oct. 1991). The agencies
both recognize the importance of the watershed approach by investing
in opportunities to advance watershed protection and in developing
useful watershed tools and services. For example, EPA is allowing
states that are reorganizing programs to function on a watershed
basis to have short-term backlogs on CWA section 402 National
Pollution Discharge Elimination System (NPDES) permit review--
without penalty. This flexibility gives states time to synchronize
the reissuance of major and minor permits within a watershed. By
managing NPDES permits on a watershed basis, all the permits for
discharges to the water body can be coordinated and the most
efficient and equitable allocation of pollution control
responsibility can be made. U.S. Environmental Protection Agency,
Why Watersheds?, EPA 800-F-96-001 (February 1996). Applying a
watershed approach continues to be a priority of EPA, and is one of
the three key strategies the agency is using to drive progress
toward the Agency's health and environmental goals over the next
five years. U.S Environmental Protection Agency, FY 2011-2015
Strategic Plan: Achieving Our Vision, 2010.

B. Similarly Situated

    Scientists routinely aggregate the effects of groups of waters,
multiplying the known effect of one water by the number of similar
waters in a specific geographic area, or to a certain scale. This
kind of functional aggregation of non-adjacent (and other types of
waters) is well-supported in the scientific literature. See, e.g.,
R.J. Stevenson and F.R. Hauer, ``Integrating Hydrogeomorphic and
Index of Biotic Integrity Approaches for Environmental Assessment of
Wetlands,'' Journal of the North American Benthological Society
21(3): 502-513 (2002); S.G. Leibowitz, ``Isolated Wetlands and Their
Functions: An Ecological Perspective,'' Wetlands 23:517-531 (2003);
D. Gamble, et al., An Ecological and Functional Assessment of Urban
Wetlands in Central Ohio, Ohio EPA Technical Report WET/2007-3B
(Columbus, OH: Ohio Environmental Protection Agency, 2007); C.R.
Lane and E. D'Amico, ``Calculating the Ecosystem Service of Water
Storage in Isolated Wetlands using LiDAR in North Central Florida,
USA,'' Wetlands 30:967-977 (2010); B.P. Wilcox, et al., ``Evidence
of Surface Connectivity for Texas Gulf Coast Depressional
Wetlands,'' Wetlands 31(3):451-8 (2011). Similarly, streams and
rivers are routinely aggregated by scientists to estimate their
combined effect on downstream waters in the same watershed. This is
because chemical, physical, or biological integrity of downstream
waters is directly related to the aggregate contribution of upstream
waters that flow into them, including any tributaries and connected
wetlands. As a result, the scientific literature and the Report
consistently documents that the health of larger downstream waters
is directly related to the aggregate health of waters located
upstream, including waters such as wetlands that may not be
hydrologically connected but function together to prevent
floodwaters and contaminants from reaching downstream waters.
    In the aggregate, similarly situated wetlands may have
significant effects on the quality of water many miles away,
particularly in circumstances where numerous similarly situated
waters are located in the region and are performing like functions
that combine to influence downstream waters. See, e.g., A. Jansson
et al., ``Quantifying the Nitrogen Retention Capacity of Natural
Wetlands in the Large-Scale Drainage Basin of the Baltic Sea,''
Landscape Ecology 13:249-262 (1998); W.J. Mitsch et al., ``Reducing
Nitrogen Loading to the Gulf of Mexico from the Mississippi River
Basin: Strategies to Counter a Persistent Ecological Problem,''
BioScience 51(5): 373-388 (2001); M.G. Forbes, et al., ``Nutrient
Transformation and Retention by Coastal Prairie Wetlands, Upper Gulf
Coast, Texas,'' Wetlands 32(4):705-15 (2012). Cumulatively, many
small wetlands can hold a large amount of snowmelt and
precipitation, reducing the likelihood of flooding downstream.
Report at 5-25 (citing D.E. Hubbard and R.L. Linder, ``Spring Runoff
Retention in Prairie Pothole Wetlands,'' Journal of Soil and Water
Conservation 41(2):122-125 (1986)).
    Scientists can and do routinely classify similar waters and
wetlands into groups for a number of different reasons; because of
their inherent physical characteristics, because they provide
similar functions, because they were formed by similar geomorphic
processes, and by their level of biological diversity, for example.
Classifying wetlands based on their functions is also the basis for
the U.S. Army Corps of Engineers hydrogeomorphic (HGM)
classification of wetlands. M.M. Brinson, A Hydrogeomorphic
Classification for Wetlands (Washington, D.C.: U.S. Army Corps of
Engineers, 1993). The HGM method is a wetlands assessment approach
pioneered by the Corps in the 1990s, and extensively applied via
regional handbooks since then. The Corps HGM method uses a
conceptual framework for identifying broad wetland classes based on
common structural and functional features, which includes a method
for using local attributes to further subdivide the broad classes
into regional subclasses. Assessment methods like the HGM provide a
basis for determining if waters provide similar functions based on
their structural attributes and indicator species. Scientists also
directly measure attributes and processes taking place in particular
types of waters during in-depth field studies that provide reference
information that informs the understanding of the functions
performed by many types of aquatic systems nationwide.
    These waters, primarily depressional wetlands, small open waters
and peatlands, are known to have important hydrologic, water
quality, and habitat functions which vary as a result of the diverse
settings in which they exist across the country. For example, a
report that reviewed the results of multiple scientific studies
concluded that depressional wetlands lacking a surface outlet
functioned together to significantly reduce or attenuate flooding.
Report at 5-26 (citing A. Bullock and M. Acreman, ``The Role of
Wetlands in the Hydrological Cycle,'' Hydrology and Earth System
Sciences 7:358-389 (2003)). Some of the important factors which
influence the variability of their functions and connectivity
include the topography, geology, soil features, antecedent moisture
conditions, and seasonal position of the water table relative to the
wetland. Report at 5-25.
    When proposing that ``other waters'' are sufficiently close and
should be considered similarly situated, it is recognized that they
are more likely to have similar influence with regard to their
effect on the chemical, physical, or biological integrity of a
downstream water identified in paragraphs (a)(1) through (a)(3). If
a water is a great distance from a group of similar ``other
waters,'' it may be performing some of the same functions as those
in the group, but their distance from each other or from downstream
(a)(1) through (a)(3) waters will decrease the probability that it
has some kind of chemical, physical, or biological connectivity to
the downstream water, assuming that conditions governing the type
and quantity of flows (e.g. slope, soil, and aquifer permeability,
etc.) are similar. Id. at 5-2, 5-41.
    Consideration of the aggregate effects of wetlands and other
waters often gives the most complete information about how such
waters influence the chemical, physical, or biological integrity of
downstream waters. In many watersheds, wetlands have a
disproportionate effect on water quality relative to their surface
area because wetland plants slow down water flow, allowing suspended
sediments, nutrients, and pollutants to settle out. They filter
these materials out of the water received from large areas,
absorbing or processing them, and then releasing higher quality
water. National Research Council, Wetlands: Characteristics and
Boundaries (Washington, D.C.: National Academy Press, 1995), p. 38.
For an individual wetland, this is most pronounced where it lies
immediately upstream of a drinking water intake, for example. See,
e.g., C.A. Johnston, et al., ``The Cumulative Effect of Wetlands on
Stream Water Quality and Quantity,'' Biogeochemistry 10:105-141
(1990).
    The structure and function of a river are highly dependent on
the constituent materials that are stored in, or transported through
the river. Most of the materials found in rivers originate outside
of them. Thus, the fundamental way that ``other waters'' are able to
affect river structure and function is by providing or altering the
materials delivered to the river. Report at 1-13. Since the
alteration of material fluxes depends on the functions within these
waters and the degree of connectivity, it is appropriate to consider
both these factors for purposes of significant nexus under this
provision.
    Numerous factors affect chemical, physical, and biological
connectivity, operating at multiple spatial and temporal scales, and
interacting with each other in complex ways, to determine where
components of aquatic systems fall on the connectivity-isolation
gradient at a given time. Some of these factors include climate,
watershed characteristics, spatial distribution

patterns, biota, and human activities and alterations. Id. at 3-33.
Recognizing the limits on the ability to observe or document all of
these interacting factors, it is reasonable to look for visible
patterns in the landscape and waters that are often indicative of
the connectivity factors, in determining what waters to aggregate.
Due to relative similarity of soils, topography, or groundwater
connections, for example, there may be a group of wetlands scattered
throughout a watershed, at similar distances from the tributaries in
the watershed and performing similar functions. It is appropriate to
assess the significance of the nexus of those waters in the
aggregate, consistent with Justice Kennedy's standard.

C. Significant Nexus

    The scientific literature regarding ``other waters'' documents
their functions, including the chemical, physical, and biological
impact they can have downstream. Available literature indicates that
``other waters'' have important hydrologic, water quality, and
habitat functions that have the ability to affect downstream waters
if and when a connection exists between the ``other water'' and
downstream waters. Report at 6-1. ``Other waters'' generally fit
into the category of unidirectional waters as described in the
Report. However, there are some unidirectional waters that are in
fact adjacent under (a)(6) to (a)(1) through (a)(5) waters (e.g.,