Given that virtually all organisms are hosts for parasites, the investigation of the combined effects of contamination and parasitism is important in the framework of aquatic bioindication procedures. To assess the impact of such multistresses at the host cellular level, we sampled parasitized zebra mussel (Dreissena polymorpha) populations from two sites in northeast France that presented different levels of contamination. Experimental groups were formed based on parasite species and host gender and tested by histochemistry and automated image analysis for biological responses, such as structural changes of the lysosomal system and neutral lipid accumulation. Infected organisms displayed smaller and more numerous lysosomes compared with uninfected congeners, and infection further elevated the effect of the chemical contamination on this biomarker. In contrast, co-infection of females with selected parasites did produce inverse results, i.e. a more developed lysosomal system and neutral lipid depletion. Our data, therefore, suggest that parasitism in zebra mussels represents a potential confounding factor in ecotoxicological studies and must be taken into account in environmental risk assessment studies.