<em>Abstract.</em>—The Willamette River is Oregon’s largest river, with a basin area of 29,800 km<sup>2</sup> and a mean annual discharge of 680 m<sup>3</sup>/s. Beginning in the 1890s, the channel was greatly simplified for navigation. By the 1940s, it was polluted by organic wastes, which resulted in low dissolved oxygen concentrations and floating and benthic sludge deposits that hindered salmon migration and boating. Following basin-wide secondary waste treatment and low-flow augmentation, water quality markedly improved, salmon runs returned, and recreational uses increased. However, water pollution remains a problem as do physical habitat alterations, flow modification, and alien species. Fish assemblages in the main-stem Willamette River were sampled systematically, but with different gear, in the summers of 1945, 1983, and 1999. In the past 53 years, tolerant species occurrences decreased and intolerant species occurrences increased. In the past 20 years, alien fishes have expanded their ranges in the river, and four native fish species have been listed as threatened or endangered. We associate these changes with improved water quality between 1945 and 1983, fish migrations, altered flow regimes and physical habitat structure, and more extensive sampling.
Rearing and migration of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a large river floodplain