Elemental carbon and nitrogen levels and isotope ratios were assessed in different biological compartments of a Northwest (NW) Mediterranean bay to trace the various sources of nutrient input from natural (river runoffs) and anthropogenic (harbor outflows, fish farms and urban sewage outfall) sources. Samples from transplanted mussels and natural sea grass communities (Posidonia oceanica leaves and epiphytes) were harvested from different locations throughout the bay during the touristic summer and rainy seasons. The results from the nitrogen analysis revealed that sewage and harbor outflow promote higher nitrogen levels, enrichment of (15)N in the tissues, and a higher seasonal variability in sea grass and epiphytes. In mussel tissues, the delta(15)N was also influenced by sewage and harbor outflow, whereas delta(13)C was influenced by terrestrial inputs. These results suggest that natural and anthropogenic nutrient inputs have a temporary and localized influence and affect the sensitivity of natural isotopic ratios to changes in hydrologic conditions, especially to rain and tourism.