Urbanization is dramatically changing nutrient and organic matter regimes in streams, yet the community and ecosystem implications often remain obscure. We assessed the consequences of sewage-derived particulate organic matter (SDPOM) for invertebrate community structure and function in a headwater stream. Using stable isotope analyses, we found assimilation of organic SDPOM to double community secondary production, and stoichiometric analyses revealed SDPOM enriched in phosphorus (P) to foster putatively fast-growing, P-rich consumers in the subsidized reach. This altered consumer-resource stoichiometry impacted both community structure and nutrient fluxes through the invertebrate community. Community structure shifted toward significantly reduced diversity and evenness in the subsidized reach and consequently toward shorter food chains. Our integration of ecological stoichiometry with stable isotope analyses and food web ecology expands the previous focus of traditional ecotoxicology and ecophysiology to an ecosystem-level appreciation of pollutant ecology.