To establish the connection between pollutant levels and their harmful effects on living resources, coastal monitoring programmes have incorporated biological tools, such as the scope for growth (SFG) in marine mussels and benthic macrofauna community indices. Although the relation between oxygen-depleting anthropogenic inputs and the alteration of benthic communities is well described, the effects of chemical pollutants are unknown because they are not expected to favour any particular taxa. In this study, the combined efforts of five research teams involved in the investigative monitoring of marine pollution allowed the generation of a multiyear data set for Ría de Vigo (NW Iberian Peninsula). Multivariate analysis of these data allowed the identification of the chemical-matrix combinations responsible for most of the variability among sites and the construction of a chemical pollution index (CPI) that significantly (P < 0.01) correlated with biological effects at both the individual and the community levels. We report a consistent reduction in the physiological fitness of local populations of mussels as chemical pollution increases. The energy balance was more sensitive to pollution than individual physiological rates, but the reduction in the SFG was primarily due to significantly decreased clearance rates. We also found a decrease in benthic macrofauna diversity as chemical pollution increases. This diversity reduction resulted not from altered evenness, as the classic paradigm might suggest, but from a loss of species richness.