The algorithm is suggested for selecting most appropriate and sensitive bioassay method to a particular type of pollution prevailing in the study area. The algorithm bases on a battery of bioassays, which necessarily includes mortality test for Daphnia magna Straus, 1820. Other approaches for comparing sensitivity of methods are selected for particular aim. The algorithm has been tested in model and for in situ samples. According to the proposed algorithm, the mortality tests for D. magna and Ceriodaphnia affinis Lilljeborg, 1900 are enough informative to assess the pollution by mineral nitrogen compounds. When prevailing contamination are mineral salts of Cu, phosphates, and pyrophosphates, a bioluminescent test with Escherichia coli Migula, 1895 has the maximum sensitivity. If the aquatic environment is polluted by Cd, Pb, Zn, oil products, organic herbicides imazetapir and imazamox, chemotactic response reduction test with Paramecium caudatum Ehrenberg, 1838 is the most sensitive. The proposed algorithm is general, but it should only be used when the prevailing contaminant is known, and its effects predominate over the effects of other compounds in the sample.