This article is devoted to the development and research of a mathematical model of water fluid dynamics with variable depth. This model describes the water flow movement, the thermodynamics of ice formation and melting, considers the Coriolis force, horizontal and vertical turbulence of the water environment, the complex geometry of the coastline and bottom, friction on the bottom and wind currents, evaporation, wind speed, and atmospheric density, and the deviation of the pressure field value from the hydrostatic approximation. The article describes the influence of the spatial distribution of temperature, salinity, ionic composition, and hydrostatic pressure on the processes of ice cover formation. The Caspian Sea-was chosen as the object of the simulation. The changes in the temperature and salinity distributions measured by the electrical conductivity of the water, considering the ionic composition of the Caspian Sea waters over a long-term period, are used as input data. Modeling the movement of water flow will allow you to respond to man-made threats in an accelerated time mode. The models of hydrodynamics presented in this paper can be adapted for other reservoirs using the appropriate geoinformation systems.