The Corps has been involved in regulating activities by others in navigable waterways through the granting of permits since passage of the Rivers & Harbors Act of 1899. At first, this program was meant to prevent obstructions to navigation, although an early 20th century law gave us regulatory authority over the dumping of trash and sewage. Passage of the Clean Water Act in 1972 greatly broadened this role by giving the Corps authority over dredging and filling in the "waters of the United States," including many wetlands.

A major aspect of the Regulatory program is determining which areas qualify for protection as wetlands. In reaching these decisions, the Corps uses its 1987 Wetland Delineation Manual (available here in PDF format).

In making decisions on whether to grant, deny or set conditions on permits, District commanders are required to consider "all factors in the public interest," including economic development and environmental protection.

Numerous relatively minor activities in wetlands are covered by regional or nationwide general permits, allowing the regulatory staff to concentrate on more complex cases. Of the approximately 1,100 people who carry out this mission, about 70% have academic backgrounds in biology and environmental sciences.