Freshwater unionids are filter-feeding animals that occur in dense, biodiverse aggregations, and are abundant in rivers in the southeastern United States. Mussel assemblages can influence stream biogeochemistry, though the magnitude of effect is dependent on species-specific traits, as well as environmental heterogeneity. To evaluate how seasonal temperature influences mussel physiological rates, we conducted a field experiment using water-tight benthic chambers in the Sipsey River, Alabama, U.S.A. We predicted that: 1) respiration, clearance, and excretion and biodeposition rates would decrease across observed species as temperatures decreased, and 2) thermally-sensitive mussel species will have disproportionately greater effects on ecosystem processes at warmer temperatures. We selected four functionally distinct species that differ in thermal tolerances and life history strategies, including federally listed Pleurobema decisum. We quantified ecosystem metabolism to evaluate species-specific differences in physiological processes under contrasting environmental conditions (summer and fall) using light-dark incubations. Additionally, we quantified seasonal and species variation in mussel biofiltration by measuring changes in algal concentrations within each chamber to calculate clearance rates. We also evaluated species and season-specific differences in excretion and biodeposition rates. Preliminary results indicate chambers containing larger-bodied species have a greater influence on clearance and respiration rates than smaller-bodied species, emphasizing the importance of species-specific biomass. This research demonstrates the role of freshwater mussels in aquatic ecosystems as a vital connection between the benthos and the water column by presenting their impacts on ecosystem functions like nutrient and suspended organic matter (e.g., algae) dynamics. It also advances methodologies for in-situ mussel research, expanding upon laboratory-based studies of mussel ecophysiological processes. By deepening ecological understanding of these organisms under natural conditions, this work provides useful information to support conservation efforts for this imperiled group of organisms.