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The paper was tested method of calculating water quality class boundaries for environmental diagnostics and standardization according to the Rybinsk Reservoir. Indicators of phytoplankton fluorescence, indicators and indicators specific structure of the content of phytoplankton pigments had been used for bioindication. The content of chlorophyll “a” and the maximum level of phytoplankton fluorescence most fully reflect the causes of ill-being able to explore the ecosystems. Water temperature, nitrate nitrogen concentration, calcium and magnesium ions contribute most to the deviation from the norm of studied indicator values in the Rybinsk Reservoir. The results indicate the possibility of a successful and priority application of biophysical bio-indicators to assess the ecological status of the water.