Positive biodiversity–ecosystem functioning (BEF) relationships observed in experiments can be challenging to identify in natural communities. Freshwater animal communities are disproportionately harmed by global change that results in accelerated species loss. Understanding how animal‐mediated ecosystems functions may change as a result of global change can help determine whether biodiversity or species‐specific conservation will be effective at maintaining function. Unionid mussels represent half of imperiled species in freshwater ecosystems globally and perform important ecological functions such as water filtration and nutrient recycling. We explored BEF relationships for 22 naturally assembled mussel aggregations spanning three river basins. We used the Price equation to partition the contributions of species richness, composition, and context dependent interactions to two functions of interests: spatially‐explicit standing‐stock biomass (indirect proxy for function) and species‐specific nitrogen (N) excretion rates (direct measure of N recycling). Random and non‐random species loss each reduced biomass and N recycling. Many rare species with low contributions to biomass contributed to standing‐stock biomass in all basins. Widespread species had variable function across sites, such that context dependent effects (CDEs) outweighed richness effects on standing‐stock biomass in two basins, and were similar to richness effects in the third. Richness effects outweighed CDEs for N recycling. Thus, many species contributed a low proportion to overall N‐recycling; a product we attribute to the high evenness and functional effect trait diversity associated with these communities. The loss of low‐functioning species reduced the function of persisting species. This novel result using observational data adds evidence that positive species interactions, such as interspecific facilitation, may be a mechanism by which biodiversity enhances ecosystem functions. Our work stresses the importance of evaluating species‐specific contributions to functions in diverse systems, such as nutrient cycling when maintaining specific animal‐mediated functions is a management goal because indirect proxies may not completely characterize BEF relationships.