For reliable mussel monitoring programmes based on biomarkers, regionally relevant reference values and their natural variability need to be known. The Baltic Sea exhibits high inter-regional and seasonal variability in physical factors such as salinity, temperature and primary production. The aim of this pilot study is to depict the effects of season-related environmental factors in a selected battery of biomarkers in two environmentally different subregions of the Baltic Sea to help establishing reference data for biochemical, cellular and tissue-level biomarkers. In order to achieve that, mussels were collected from reference sites in Kiel (Germany) and Tvärminne (Finland) during three seasons: summer and autumn 2016, and spring 2017. Finally, in order to characterize the ecological situation, analysis of the chemical tissue burden was performed and chlorophyll‑a and particulate organic carbon concentration and temperature changes were analyzed at each sampling locality using satellite remote sensing images. An integrated biomarker response index was performed to summarize the biomarker responses of each locality and season. The biochemical endpoints showed seasonal variability regulated by temperature, food supply and reproductive cycle, while among the cellular endpoints only lipofuscin accumulation and lysosomal structural changes showed slight seasonal variation. Seasonal changes in tissue level biomarkers were observed only at the northern Baltic Sea site Tvärminne, dictated by the demanding energetic trade-off caused by reproduction. In conclusion, the characterization of the ecological variables and physico-chemical conditions at each site, is crucial to perform a reliable assessment of the effects of a hypothetical pollution scenario in the Baltic Sea. Moreover, reference levels of biomarkers and their responses to natural environmental conditions must be established.