Using a comprehensive approach, intertidal, near- and offshore sites in the German Bight were analysed for their environmental quality by assessing the health of blue mussels (Mytilus edulis). During a ten month sampling period mussels were studied with a set of biomarkers comprising lysosomal membrane stability and accumulation of lipofuscin, supplemented by biomarkers indicating nutritional status such as neutral lipids and glycogen in the cells of the digestive gland. Data were analysed in relation to sex, gonadal status, condition index and for the presence of parasites, to determine the overall health status of mussels at the respective sites. Mussels from all sites showed clear signs of stress, indicating an inferior environmental quality throughout the southern German Bight. Further, habitat characteristics such as inundation time and growing on- or off-bottom, as well as seasonal factors, can clearly influence the response of biomarkers in mussels exposed to similar levels of chemical environmental stress.