In addition to the clean water requirement hurdles faced by small communities, the federal Clean Water Act also places sometimes burdensome requirements on development projects which impact waters that fall under statutes of the Act. The U.S. Army Corps of Engineers implements the regulations of the Act on a project-by-project basis and generally requires on-site mitigation that can end up rendering a project fiscally infeasible. This is especially true for projects that are within the urban footprint, where there is often no possibility for on-site mitigation. This piecemeal mitigation approach runs in conflict with the U.S. Fish and Wildlife Service mandate to preserve resources in a contiguous fashion. It also can cause developers to look beyond the urban edge to find lands where development and mitigation can comply with federal standards, thereby creating development that generates longer commutes and more emissions.

The Corps' regulatory guidance to implement the Clean Water Act also affects rice farmers who can face possible regulatory action if a property is determined to be a wetland and waters of the United States. In those cases, farmers who wish to convert their land to another agricultural or non-agriculture use are faced with a burden of proof that can require them to leave their land dry and fallow for up to five years. The effects not only impact the economic viability of this farmland, but also the habitat that annually supports the most abundant array of migrating waterfowl in North America.