The continued global loss of biodiversity highlights the importance of understanding how species loss may impact ecosystem function. Shifting temperatures will accelerate species loss, but will affect species differently. We investigated effects of temperature (10°C, 20°C, or 30°C) on resource acquisition and assimilation (clearance rate, respiration rate, N and P excretion) for 11 freshwater mussel species from a species-rich assemblage in the Sipsey River, Alabama, U.S.A., to evaluate how temperatures impact co-occurring species and the ecosystem processes they facilitate. Mussels are assigned to the same guild (i.e., filter-feeding bivalves), but span a breadth of evolutionary lineages and have a diversity of life history strategies from short-lived, quickly maturing species to long-lived, slow-growing species. Our results indicated that four species (Cyclonaias asperata, Elliptio arca, Lampsilis ornata, and Obovaria unicolor) were thermally sensitive at 30°C, using more energy than they were acquiring. These species spanned three phylogenetic tribes and two different life-history strategies suggesting thermal tolerance may not necessarily be linked to life history strategy or phylogenetic constraints. When laboratory clearance and excretion rates were scaled to a natural mussel community over a year, we found that relative contributions by the proportion of thermally tolerant and sensitive species to total ecosystem function varied temporally across temperature and flow regimes. Thermal stress enhanced contributions by sensitive species’ during summer, as individuals attempted to meet metabolic demands by increasing clearance rates and use of energy stores that increased ammonia excretion. River discharge and background nutrient concentrations also modulated the impact of ecosystem functioning facilitated by mussels. High river discharge in winter and high background nutrient concentrations in the summer decreased the relative contribution of the mussel community. Although mussel species are commonly grouped in a single guild, species-specific thermal traits modulate their role in the community. As biodiversity decreases, even biomass replacement by surviving mussel species is unlikely to support comparable ecosystem function due to the loss of unique species traits.