During the study of hydrophysical processes, thermohaline measurements are usually carried out at a limited number of points. Thus, determination of seawater salinity at an arbitrary point of the reservoir on the basis of observed values is an interesting problem from the scientific point of view. Below, we describe the solution of this problem using mathematical modeling. The mathematical model of processes of matter transport and spreading in water consists of two components: a hydrodynamic model of the reservoir and a model describing convective-diffusive transport of a substance. The shallow reservoir of the Sea of Azov (up to 14 m), commonly accepted as a basin with a flat even bottom, is of a certain scientific interest. Actually, new large-scale charts demonstrate strong differentiation of the bottom topography in the coastal shelf and open sea regions [2]. Equations for shallow water are usually used for the calculation of currents in shallow basins, while currents in the deep basins are modeled by 3D equations of fluid motion. If a reservoir has large, shallow and sufficiently deep regions, application of shallow water equations will not yield a reliable pattern of currents in the deep-water part of the basin. At the same time, application of 3D equations for the entire basin can require the use of curvilinear grids (at least over the vertical) or preliminary transformation of the initial irregular domain into a regular one. Such transformations strongly complicate the formulation of the problem and its numerical solution. However, if we identify domains of shallow and deep zones of the basin, it is possible to apply the shallow-water equations and 3D equations of fluid motion without preliminary transformation of the calculation area. In this case, it is possible to use the finite difference methods using uniform rectangular grids, which undoubtedly simplifies the solution of the problem. The advantage of the model applied here is its simple mathematical description and easy numerical realization especially using the algorithms of parallel computation. The initial 3D modeling domain is the water medium of the basin limited from above and below by the sea surface and seafloor, respectively. Let us locate a horizontal secant plane P at a distance from the unperturbed surface of the basin P 0 at a depth equal to the maximal depth of the shallow region and divide the entire modeling domain into the upper (I) and lower (II) layers (Fig. 1). Layer I includes the entire coastal zone and the upper layer of the open sea. Layer II is the lower layer of the water column. The motion in layer I is described by the shallow-water equations: