Freshwater unionid mussels play important roles in many key ecosystem functions (i.e., nutrient dynamics and ecosystem metabolism), however, their species-specific roles in these processes remain understudied. Freshwater mussels are imperiled across much of North America, and declines in mussel populations may result in cascading losses of mussel-mediated nutrient and organic matter provisioning. Given the high trait diversity among mussel species, shifts in the composition of mussel assemblages may alter mussel-mediated nutrient cycling rates and other processes. To understand the role of freshwater mussels on ecosystem function, we conducted in situ experiments in a stream with high mussel diversity in the southeastern USA. Using experimental chambers, we quantified how different mussel species and assemblages shape net N2 exchange, net nutrient (nitrogen and phosphorus) fluxes, ecosystem respiration, and net ecosystem production. We paired these measured rates with species-trait data to assess how species-specific traits drive mussel-mediated ecosystem processes. We expected that mussels would increase organic matter content by supplying carbon-rich biodeposits, and therefore enhance denitrification rates (positive N2 flux to water); however, N2 exchange did not differ among species treatments. Mussel-mediated dissolved nutrient fluxes between sediments and the water column varied among species treatments, likely linked with burial depth and nutrient excretion rates. However, ambient nutrient uptake processes in this nutrient-limited stream likely offset nutrients supplied by mussels. Additionally, mussels enhanced ecosystem respiration and gross primary production rates while exerting minimal influence on net ecosystem production. Mussel traits including biomass and nutrient excretion rates were important factors in determining ecosystem respiration and gross primary production, which exemplifies the importance of trait differences in mussel-mediated ecosystem processes. This study highlights the complex roles freshwater mussels play in mediating biogeochemical processes in situ and emphasizes the importance of considering how biodiversity shapes ecosystem function. Understanding mussel-mediated ecosystem processes is crucial for conserving both mussel biodiversity and associated ecosystem services.