As human civilization develops, environmental problems arise more and more often. All forms of the environment are consistently exposed to pollution: water, air, and soil. In the natural aquatic environment, redox processes occur, in which both endogenous and exogenous substances are involved. The processes of antagonism and synergy are also realized, which leads to a decrease or increase in the toxicity of the environment. All this affects intra-aquatic processes, which, as a result, lead to the formation of the quality of the aquatic environment. Historically, there have been three main approaches to assessing water quality using biological objects. These are biodiagnostic methods: bioindication, bio marking, and biotesting. The review reveals the features of biodiagnostic methods and their application in assessing the quality of natural waters.