The Clinch River in Virginia and Tennessee, USA, is well known for its diverse native freshwater mussel assemblages; however, notable declines in mussel populations in recent decades have prompted much concern and subsequent research. We examined the toxicity of recently-deposited sediments on juveniles of the freshwater mussel Epioblasma brevidens, by collecting time-integrated sediment samples from the water column with sediment traps from 11 sites in the Clinch River Basin, including 6 sites within an 88-km reach deemed a ‘mussel zone of decline’. Mussels were exposed to the riverine sediments and to 3 control sediments for 28 d; survival, shell length, and biomass were then assessed. Sediment treatment (i.e., river location) had a significant effect on mussel survival (p < 0.01) and biomass (p = 0.02), but did not affect length (p = 0.37), and sediments from 2 of the tributaries were the most toxic. Inorganic and organic analyses of sediments indicated the presence of metals and polycyclic aromatic hydrocarbons at all sites. Manganese was negatively correlated with mussel survival and biomass, as was ammonia with survival, and total organic carbon with biomass. Current land uses in the watershed indicate that fossil fuel mining and agriculture may be associated with elevated manganese and ammonia, respectively. We found that sediments collected with sediment traps over relatively short deployment durations can help elucidate recent contaminant influx and its potential for inducing toxicity in benthic organisms.