The linkages between biological communities and ecosystem function remain poorly understood along gradients of human-induced stressors. We examined how resource provisioning (nutrient recycling), mediated by native freshwater mussels, influences the structure and function of benthic communities by combining observational data and a field experiment. We compared the following: (1) elemental and community composition (algal pigments and macroinvertebates) on live mussel shells and on nearby rocks across a gradient of catchment agriculture and (2) experimental colonisation of benthic communities on live vs. sham shells controlling for initial community composition and colonisation duration. We show that in near pristine systems, nutrient heterogeneity mediated by mussels relates to greater biodiversity of communities, which supports the notion that resource heterogeneity can foster biological diversity. However, with increased nutrients from the catchment, the relevance of mussel-provisioned nutrients was nearly eliminated. While species can persist in disturbed systems, their functional relevance may be diminished or lost.