 His early career included surveying the Patapsco River, sounding and mapping the approaches to New Orleans, and surveying Portsmouth Harbor.From 1844 to 1849 he was assigned to a survey of the northeastern boundary of the United States, serving under James Duncan Graham.In 1848 Whipple was assigned to the United States Boundary Commission, tasked with surveying the new boundary between the US and Mexico resulting from the Mexican–American War.