The main-stem Allegheny River is nationally recognized for its freshwater mussel (Unionidae: Bivalvia) diversity; however, habitat disturbance and degradation may have triggered the decline and loss of mussel communities in the lower river, where lock and dam structures restrict the free flow of water and sand and gravel removal threaten limited habitat. We examined mussel diversity and abundance across 75 transects throughout navigational pools and recorded 21 live native mussel species, including federally endangered Pleurobema clava (Clubshell) and Epioblasma torulosa rangiana (Northern Riffleshell) and several species with state endangered or threatened status. Riverine species richness and counts were significantly higher in the most-upstream portions of the upper pools, indicating that areas with consistent flows and suitable substrate just downstream of the dams may provide refugia for riverine freshwater mussel species. Sand, gravel, cobble, boulder, and organic debris had significant positive effects on riverine and facultative counts, while clay, bedrock, and woody debris had significant negative effects. Silt and woody debris had significant negative effects on riverine species richness, and sand and gravel had significant positive effects. These data will help identify sensitive areas for future protection and provide baseline data for monitoring future trends. The protection of relatively shallow areas with suitable substrates not yet impacted by dredging operations will be important to sustain remaining freshwater mussel populations in these pools.