A hydrophysics mathematical model of a shallow water body is proposed, including the pollutants (PS) transport equation, taking into account their gravitational settling, numerically implemented in the software module form. The developed software module makes it possible to evaluate the pollutant concentrations distribution during their deposition from the aquatic environment surface. A model for predicting the distribution of pollutants along the vertical coordinate in a reservoir is proposed, taking into account the movement of the water environment.