This article is devoted to planning water-energy regimes for hydropower plants, taking into account economic and ecologic criteria. A new methodology based on a probabilistic model of water inflow has been proposed. The probabilistic method requires the calculation of low-water and average-water year typical hydrographs based on the probability curve. This allows the determination of the guaranteed hydropower plant generation schedule with a month time-step. According to the method considered, the mathematical model of the reservoir filling and normal power station operation has been designed. The software for the automated water-energy mode calculation is presented in this paper. The economic feasibility of maximum replacement of thermal power plants in the energy system with more environmentally friendly hydropower plant is substantiated. The methodology of water resources cost calculation and economic efficiency assessment under various hydropower plant regime scenarios have been proposed in the paper. Using the data and characteristics of HPPs and TPPs, an assessment of energy efficiency will be obtained in accordance with the developed methodology to determine the price of water for HPPs and all participants in the water management complex. The results of the implementation of the developed approach indicate that the price of electricity sales in a competitive electricity market can be brought into line with the price of electricity sales generated by thermal power plants, which increases the economic feasibility of the maximum replacement of thermal power plant capacity in the system with more economical and environmentally friendly hydropower plant. The developed method allows for an increase in the efficiency of water resources use and the efficiency of hydropower plant participation in the energy balance, which makes it possible to displace part of the power generated by thermal power plants.