Nearshore water quality can be highly impacted by anthropogenic activities ongoing along the coast, the effects of which on natural environments can be permanent and irreversible, with consequences for ecosystem biodiversity and functioning, as well as for associated services. Benthic filter feeders (e.g., mussels) provide several services for coastal regions, including improving water quality by reducing eutrophication, being a major source of food for humans, and as a habitat-forming species. Here, we seek to understand the role of benthic filter feeders in enhancing water quality in an urban coastal system in order to assess their role as ecosystem service providers and how they should be included in ecosystem-based evaluations. Using as a model False Bay, South Africa's largest natural bay and a socioeconomic hotspot, this multidisciplinary study was designed to identify possible pollution sources to a highly-urbanised coastal region, assess their effects on several biological and biogeochemical parameters, and evaluate the role of mussels in mitigating these anthropogenic inputs. We consider several sources of pollution, including nutrient loading from wastewater and river outflows, heavy metals, and aerosol deposition. We find that pollutant inputs are largely attenuated by the circulation of the bay and by the presence of filter feeders that bioaccumulate contaminants, thereby removing them from coastal waters. Our work thus emphasizes the potential for mussels and natural abiotic processes to ameliorate anthropogenic impacts, although these mitigation strategies are not without environmental risk. We recommend that such information should be included in national assessments used to develop appropriate strategies and policies for coastal environmental management and conservation.