Freshwater mussels in the western US are under-studied compared to their eastern cousins, and no western species receive federal protection. Mussel distribution throughout Oregon's rivers and streams is poorly documented, and there are limited historical records to inform assessments of whether, and by how much, current populations may have declined. We launched a long-term project to characterize freshwater mussel populations throughout the Willamette River basin. Surveys were conducted in the mainstem Willamette River and a major tributary, the Middle Fork Willamette, during three years. A two-stage sampling process was used; transects were surveyed qualitatively, and then 0.25 m² quadrats were placed randomly in transects for quantitative surveys. Mussels visible at the substrate surface were counted using viewing scopes and snorkeling, and scuba diving in deeper water. To facilitate detection of juveniles (≤ 3.50 cm long) and calculation of the burial factor, some quadrats were double sampled; mussels visible at the surface were counted, then the substrate was excavated to a depth of 10 to 20 cm, and all mussels (surface and buried) were counted and their shell length measured. Dense western pearlshell (Margaritifera falcata) populations were found at all locations, but they differed greatly in length class structure, density, and presence of juveniles. Some sites also contained small numbers of floaters (Anodonta spp.), and notably, a single western ridgemussel (Gonidea angulata) was found in a highly urbanized reach. These surveys provide baseline data on the current status of several freshwater mussel populations in the Willamette River basin.