In freshwater ecosystems, animals can play large roles in biogeochemical cycles by sequestering and recycling nutrients and by modifying their physical habitat. Nutrient release from consumers can support both ‘green food webs' based on primary producers and ‘brown food webs' based on decomposers. Microbes also play a critical role in facilitating biogeochemical processes, such as the nitrogen cycle, in which they transform organic and inorganic nitrogen compounds. Freshwater mussels (Bivalvia: Unionoida) are a guild of benthic, burrowing, filter-feeding bivalves that translocate nutrients and energy from the water column to the benthos via excretion and egestion. Despite being classified in the same functional group, mussels within the same system exhibit variation in functional traits such as nutrient stoichiometry and burrowing behavior which can strongly influence ecosystem processes. Therefore, quantifying functional trait diversity is key to improving our ability to predict the effects of mussel diversity loss on ecosystem function. Here, we used a mesocosm experiment to investigate how phylogenetically diverse mussel communities influence ecosystem functioning through direct and indirect effects. Our results suggest that mussel-mediated nutrient cycling directly influences brown and green food webs by increasing primary productivity and enhancing organic matter decomposition. Additionally, mussels physically (via bioturbation) and chemically (via excretion and egestion) influenced sediment-water nutrient fluxes and sediment microbiome community composition by increasing sediment nitrogen-removal potentials. Our study advances our understanding of how mussel species identity and community composition regulates components of green and brown food webs as well as potentially predicting changes in ecosystem functioning as a result of a loss or shift in species composition.