In addition to pollution, organisms are exposed to natural variations of the biotic and abiotic factors of their environment. A battery of sub-cellular biomarkers has been measured seasonally in several populations of both Dreissena polymorpha and Dreissena rostriformis bugensis. To observe and understand the variability associated with biomarker responses, water physico-chemistry, sediment contamination and internal concentrations of contaminants in soft tissues were also considered. Results evidenced seasonal, inter-specific and inter-populational variability of the measured responses, highlighting the needs (1) to acquire long-term data on the studied populations and (2) to incorporate environmental parameters and contamination in the interpretation of biological responses. From a biomonitoring perspective, significant relationships were identified between biomarkers, internal concentrations of contaminants in soft tissues and sediment contamination in D. r. bugensis and, to a lesser extent, in D. polymorpha. The detailed interpretation of each biomarker of the battery measured is complex, but a global analysis of all biomarkers at once allows to obtain this signature of the contamination of the studied sites.