In the practice of using river resources accumulated in reservoirs, there is a typical problem of unreasonably large water intake for industrial-household needs to the detriment of the aquatic ecosystem. An important tool for balancing these links is to provide environmental flows based on a comprehensive analysis of river functioning patterns. And in terms of a progressing negative impact of reservoirs on the integrity of river ecosystems, the choice of indicator hydrobiota for the calculation of environmental flows should be considered insufficiently substantiated. The solution of this problem, by filling the appropriate methodological niche, allowed substantiating the hydrological-stenobiontic method for determining environmental flows. The developed solutions are based on the minimum possible values of tolerance of aquatic ecosystems stenobionts to water velocity. Five groups of macrozoobenthos represent relevant target organisms. The hydrological calculations presented in the paper are based on the data of daily water flow rate for 80 years and the results of field studies of the river channel depth in the low water period. On this basis, it was determined that for lowland parts of rivers, the flow velocity in the tailwater of reservoirs should be at least 0.2 m/s. Comparison of the curve of the average monthly water velocity dynamics of 95 % runoff availability with the minimum corresponding requirements of stenobionts allowed determining the most threatening period of the year for the aquatic ecosystem – summer low water. For a reservoir in the lowland parts of the river, based on the developed method, the calculations substantiate an increase in the minimum volume of environmental flows by 40 % relative to the current one. It is also estimated that the average annual and average second volumes of environmental flows should be about 38 % of the respective river runoff. The obtained results are close to those found on rivers in China, Iran and the United States in the framework of a comprehensive analysis of hydrological, hydraulic and hydrobiological parameters of the aquatic ecosystem