Despite a long history of human manipulation, the most dramatic changes in the upper Mississippi River occurred in the 1930s with construction of a lock and dam system to facilitate the commercial transport of commodities. In 1988, barge traffic through the system ranged from 7,500 tows per year at Lock and Dam 26 (near Alton, Illinois) to 1, 118 at Lock and Dam 1 (in Minneapolis/St. Paul). The tow-teed dam system created a diversity of lentic habitats, but it also changed the stage and sediment transport characteristics of the river. The principal fishery-related water quality issues of this modified system concern the effects of sediments and toxic contaminants from nonpoint sources. Between 42 and 99% of the streams in the five states of the Mississippi River basin fail to fully support their designated uses because of pollution. primarily from nonpoint sources (e.g., 73% in Minnesota, 98% in Wisconsin, 75% in Illinois). Annual sediment inputs into the upper Mississippi River basin range from minimal in the upper reaches to about 210.000 kg/hectare in the lower reaches. This sediment results in significant losses of fishery habitat. Although bnly 5 to 9% of the total open water area of many pools had been lost by 1975, those losses were in highly productive side channel and backwater areas. Under existing conditions, a loss of an additional 22 to 49% of existing lentic habitats is predicted within 50 years. In addition, toxic contaminants transported along with fine sediments have become more available to stream biota. Although significant interagency efforts have been made to evaluate the impacts on biotic communities of the river. present data are inadequate to determine how changes in water quality affect the fisheries. This lack of data undermines our ability to judge the success of programs initiated to control pollution from point and nonpoint sources.