The problem of developing early diagnostic tools for bioindication of the state of aquatic ecosystems and assessment of pollution level dangerous for the environment and biota is of great importance. The BEAST project of the Baltic Sea BONUS programme develops approaches for the assessment of ecosystem health in different regions of the Baltic Sea. Among other goals the project contributes to clarifying linkages between biological responses in organisms and effects at population level caused by environmental contamination to develop integrated indicators for ecosystem health assessment. In BEAST, SRCES RAS has carried out studies contributing to ecosystem health assessment basing on evaluation of the physiological state of organisms by the means of noninvasive fiber-optic monitoring of heartbeat of selected invertebrate species (Mytilus edulis, Macoma balthica, Carcinus maenas). During the 2 years of the project the SRCES activities were focused to test organisms in the field in different sub-regions of the Baltic Sea, including measurements on board of research vessels and in the laboratory. The data obtained have led to the improved characterization of cardio-vascular system responses in mollusks and crabs under standard test stimuli and the development of new biomarkers based on heart rate of aquatic invertebrates. Responses to treatments with standard test stimuli provide integral information of the adaptive capacities of organisms. The results of these studies demonstratedsignificant geographical variability in cardiac responses in organisms related to the ecological/pollution status of the studied sites. Conclusively, the system for non-invasive monitoring of heart rate and its variability in selected invertebrates developed and tested under the BEAST project can be applied as an early diagnostic tool and contributes to the assessment of ecosystem health.The work was supported by RFBR grant № 08-04-92424-BONUS_a.