Summary: Mathematical models of hydrothermal processes for stratified flows in flow-through reservoirs are considered in the paper. Models are based on the equations of fluid mechanics and heat transfer. They are applied to describe the hydrothermal regime of the Krasnoyarsk reservoir. It is assumed that the reservoir depth is varied continuously, and the reservoir width is varied in a stepwise way. A numerical algorithm to study two-dimensional vertically stratified flows in terms of the streamfunction and the vorticity is considered. Parametrization of coefficients of the vertical turbulent exchange is proposed. Numerical results for currents at the dam area of the Krasnoyarsk reservoir are presented. The numerical model allows one to determine the temperature of water entering the intake openings in relation to the stratification, the position of water intake and the flow rate of water.