COE's administration of the Section 404 program has changed significantly in recent years, the program at best has become a tool for retarding the loss of and protecting aquatic ecosystems, not for restoring them, with the incidental exception of some restoration mitigation projects. Further, the Clean Water Act of 1977, despite its objective including physical restoration, established no programs for EPA or COE to use to pursue actual physical restoration of aquatic ecosystems.

Over the last 20 years, the nation has made considerable progress in controlling and reducing certain kinds of chemical pollution of its rivers, lakes, and wetlands. Biological oxygen demand loadings from sewage treatment plants have been reduced significantly. Direct industrial discharges have been controlled. The use of certain agricultural pesticides, such as dichlorodiphenyltrichloroethane (DDT) and other chlorinated hydrocarbons, has been restricted or banned. As a result, the chemical water quality, including dissolved oxygen (DO) levels, in many lakes and rivers has improved, and loadings of some toxic contaminants have decreased.

At the same time, it is well recognized that the nation's water quality programs have not been effective in controlling and reducing loadings of nutrients, sediments, and some toxicants associated with "nonpoint source" pollution from agricultural, urban storm water discharge, mining, and oil and gas extraction activities. This kind of pollution results typically from material changes in the landscape or watershed of affected aquatic ecosystems—removal of forests or other native vegetation, diversion and replacement by exposed soil or impervious material—coupled with dispersed addition of agricultural or lawn fertilizers, animal manure, and other chemicals. Airborne contaminants, including sulfate, nitrate, and metals, add to these nonpoint source loadings. The 1990 amendments to the Clean Air Act should contribute to reducing these atmospheric inputs. The causes of nonpoint source pollution suggest that restoration of the land surface within aquatic ecosystem watersheds on a landscape basis may be one strategy to reduce loadings of sediments, nutrients, and toxicants. However, limited attention has been paid to aquatic ecosystem restoration as defined in this report; the Clean Water Act's mandate "to restore..." was confined to a particular and, from an aquatic ecosystem perspective, narrow focus on chemical pollution, concerns in Section 404 about the evolution of wetlands notwithstanding. Within this limited domain there has been success, but challenges remain.

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