Toxic chemicals introduced into the environment can penetrate ecosystems and can be found in the whole biosphere. Chemical contamination may affect ecosystems, causing changes in the functions of particular organisms. Adverse effects of xenobiotics and their metabolites on living organisms can be observed. In the last few years investigations have focused on searching for bioindicators (both plant and animal organisms) that accumulate toxic substances. The aim of the present study was to discuss selected methods of environmental quality assessment based on living organisms used as bioindicators, paying special attention to water ecosystems.