Freshwater mussels are thought to have declined in abundance and changed in species composition in the Columbia River in recent years. We surveyed the 118 km of river between Vernita Bridge and Wallula Gap and found only two small aggregations of floaters (Anodonta spp.) and no western pearlshell mussels (Margaritifera falcata), a species which was formerly dominant in the river. One of the floater aggregations appears to have been nearly extirpated but may be recovering, while the other aggregation appears to be stable. Scattered individual floaters were also found in McNary Reservoir. Two populations of western pearlshell mussels were studied in the Clearwater River in Jefferson County, WA for comparison. The Clearwater populations were large, densely aggregated, of multiple size classes, and showed little evidence of mortality. Mussel tissues from each site were analyzed for lipid content and levels of arsenic, mercury, and organochlorine pesticides. The highest lipid content and mercury concentration were found in mussels from the Clearwater River. Arsenic concentration and organochlorine pesticides were highest in mussels in the Columbia River. Overall, the mussel aggregations within the Columbia River were small, scattered, and provided a marked contrast to the flourishing mussel beds in the Clearwater River. These results suggest that Columbia River mussels have both declined and changed in species composition over the last century.