The use of biological objects in monitoring the state of the environment and the changes caused by the impact of environmental pollution on marine and fresh waters is a promising tool due to a lower cost in comparison to traditional monitoring and the ability to receive immediate information about the ecosystem status. In this review, we summarize the biological information about shellfish biomonitors and the results of studies focused on the development and use of the bioindicator species in early warning systems in Russia. Since the mid-1980s, Russian specialists have developed online biomonitoring systems; as in the rest of world, there are two main approaches that are currently applied to study the physiological status of potential biosensor shellfish species and to monitor freshwater and marine systems: valvometry (registration of gaping activity in bivalve mollusks) and photoplethysmography (registration of cardiac activity in mollusks and crustaceans). Valve movement responses to stressors such as abnormal conditions and pollutants include the closure of shell valves for a long period, decrease in the average distance between valves, rapid shell opening, and higher closing frequency. Cardiac activity reactions of shellfish to stress factors include rapid increases in heart rate and stress index, higher variability in heart rate than under normal conditions, and longer periods required for heart rate recovery after stress. The most common bioindicators used to monitor environmental disturbances in marine ecosystems are blue mussels, Iceland scallops, and red king crabs in cold-water habitats and Black Sea mussels in warmer waters as well as freshwater mussels and crayfish in fresh waters.