The neutral red retention (NRR) assay to determine lysosomal membrane stability (LMS) was applied to wild mussels (Mytilus galloprovincialis) sampled from fourteen sites with different degrees of chemical pollution along the Iberian Mediterranean coast in 2002 and 2003. Total body burdens for a range of contaminants were measured in pooled samples (n = 50) of whole soft tissues in order to explore possible causality. Mean LMS values (n = 15) were significantly greater in mussels from one of the selected two reference sites (San Diego) than in chemically well-characterized hotspot sites. Mean LMS values were inversely correlated with contaminant concentrations in mussel tissues (except for Zn). The multidimensional scaling ordination technique classified the sampling sites into three groups according to their chemical-physical-biological similarities and the results were statistically confirmed using ANOSIM analysis. The results show that lysosomal stability is an effective indicator of health status in mussels along the Iberian Mediterranean coast and that it is related to body burden of contaminants, particularly polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs).