A survey of the fish assemblages between river kilometer 283 and 2 of the mainstream Willamette River, Oregon, was conducted in 1983 to evaluate the effects of improved water quality on longitudinal changes in fish assemblages and the usefulness of two indices of fish assemblage quality (index of well being and index of biotic integrity). Physical and chemical habitat quality and fish assemblage quality showed gradual, similar, and expected declines from the upper to the lower river, with only small changes near large point sources of pollution. More fish species, more species intolerant of poor habitat quality, and fewer species tolerant of poor habitat occurred in 1983 than in 1945. Stream order was not a predictor of fish assemblage patterns. A modification of the index of biotic integrity appeared to reflect changes in fish assemblage patterns and habitat quality better than the index of well being. (Copyright (c) by the American Fisheries Society 1987.)