Stress biomarkers, which can outline impacts of contaminants in aquatic biota at the biochemical level, are increasingly used as early warning tools in environmental monitoring. Reliable biomarker based assessment schemes, however, request appropriate knowledge of baseline levels of selected endpoints, and the potential influence of a range of natural influencing factors (both abiotic and biotic) as well. In this study, we examined the interspecies variability of various biomarkers (metallothioneins (MT), ethoxyresorufin-Odeethylase activity (EROD), lipid peroxidation (LPO), DNA strand breaks (DNA_sb), vitellogenin-like proteins (Vtg)) in Dreissena polymorpha and Dreissena bugensis inhabiting either pristine-or moderately impacted sites of Lake Balaton (Hungary). Levels of all biomarkers considered revealed low interspecies variability in the two dreissenid species at all sampling sites, with consistently higher (but statistically insignificant) values in Dreissena polymorpha. Levels of all biomarkers varied within the two investigated seasons, with significant influence of the reproduction cycle particularly on the levels of metallothioneins and vitellogenin-like proteins. Each biomarker considered was elevated by October, with significantly higher values in the mussels inhabiting harbours. Insignificant spatial and temporal variability in the general health indicators (condition index, total protein content) of dreissenids was observed, which, in parallel with evident rise in biomarker levels, apparently suggest that the anthropogenic impacts in harbours affect mussel fitness yet at sub organismal level. Our data might serve useful basis for future environmental monitoring surveys, especially in habitats where the progressive replacement of Dreissena polymorpha by Dreissena bugensis is taking place, as the interspecies variability in susceptibility to chemical stress of the two species is well comparable.