In this study the effect of inputs of organic matter and anthropogenic nitrogen at small spatial scales were investigated in the benthos of the Ria of A Coruña (NW Spain) using stable carbon and nitrogen isotopes. This ria is characteristically enriched in nutrients provided either by marine processes (as coastal upwelling) or by urban and agricultural waste. Stable isotope composition in trophic guilds of infaunal benthos revealed spatial differences related to their nutrient inputs. The main difference was the presence of an additional chemoautotrophic food web at the site with a large accumulation of organic matter. The enrichment in heavy nitrogen isotopes observed in most compartments suggests the influence of sewage-derived nitrogen, despite large inputs of marine nitrogen. Macroalgae (Fucus vesiculosus) resulted significantly enriched at the site influenced by estuarine waters. In contrast, no differences were found in mussels (Mytilus galloprovincialis), thus suggesting a major dependence on marine nutrient sources for this species. However, the estimations of anthropogenic influence were largely dependent on assumptions required to model the different contributions of sources. The measurement of stable isotope signatures in various compartments revealed that, despite anthropogenic nutrients are readily incorporated into local food webs, a major influence of natural marine nutrient sources cannot be discarded.