States are responsible for submitting periodic water quality assessment reports—Section 305(b) reports—and lists—Section 303(d) lists—of impaired waters to the EPA. They then are supposed to restore impaired waters by developing Total Maximum Daily Loads (TMDLs), which are limits that in theory, if fully implemented, should ensure that the state’s waters achieve the relevant quality standards. The EPA establishes federal guidance water quality criteria and oversees the establishment of state water quality standards to ensure that they are consistent with the requirements of the Clean Water Act, including ensuring that state-adopted water quality criteria are sufficient to attain the designated uses assigned by the state.The EPA also oversees state National Pollutant Discharge Elimination System (NPDES) permitting, issuing NPDES permits to dischargers in states that have not assumed this permitting authority and helping to resolve interstate water pollution issues. Finally, the U.S. Army Corps of Engineers implements the “dredge-and-fill” (wetlands) permit program in almost all states, subject to EPA oversight.

The Clean Water Act (CWA) is a lengthy and complex body of legislation, and this chapter does not attempt to examine all of its provisions. Instead, for purposes of this report and its emphasis on the Mississippi River, the chapter focuses on the CWA sections and the federal and state authorities and responsibilities that are important in understanding Clean Water Act applications and challenges along the Mississippi River. This report focuses on point and nonpoint source pollution of the mainstem Mississippi River, not ancillary issues that may arise with regard to the dredging and filling of wetlands. As a result, at the federal level, this report focuses on EPA’s regulatory authority, not that of the Corps of Engineers. The EPA’s jurisdiction to regulate discharges of pollutants into the Mississippi River and its major tributaries is clear, despite recent U.S. Supreme Court decisions and agency guidance regarding the extent of federal jurisdiction over wetlands and isolated waters. This chapter also discusses interstate and federal-state water quality interactions and the relevance of the CWA to these interactions. The chapter is divided into four sections: origins of the Clean Water Act; Federal Water Pollution Control Act amendments of 1972; state-level authority in protecting water quality; and interstate water quality protection.

Congress enacted the Rivers and Harbors Act of 1899 to preserve and enhance navigation in the nation’s waters. Section 13, the Refuse Act, prohibits pollution of the nation’s “navigable waters.” The language of Section