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 physicochemistry, 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.