Two mathematical methods to assess the “health status” of flounder (Platichthys flesus), eelpout (Zoarces viviparus) and blue mussel (Mytilus spp.) populations of the Baltic Sea were applied on selected biomarker data collected during the EU project “BEEP” (Biological Effects of Environmental Pollution on Marine Coastal Ecosystems). The Bioeffect Assessment Index (BAI) and the Integrated Biomarker Index (IBR) combine different biomarkers to single values, which can be used to describe the toxically-induced stress level of populations in different areas. Both indices determined here produced essentially similar results, which in most cases agreed with the known contamination levels in the different study areas. Advantages and limitations of index applications and interpretations are critically discussed. The use of indices provides comprehensive information about biological effects of pollution in marine organisms and may therefore serve as a useful tool for environmental management by ranking the pollution status of marine coastal areas.