The article is concerned with the problem of the motion of two layers of an ideal incompressible heavy fluid above deformable bottom. The modeled medium is taken as three layers - two layers of homogeneous fluid and a bed layer. Two upper layers of liquid are considered as homogenous. The corresponding system of nonlinear differential equations with boundary conditions is integrated analytically resulting in determination of basic hydrodynamic characteristics of the dynamic process under study, as well as the shapes of interfaces and bottom surface. The presented hydrodynamic characteristics in combination with experimental data can define the shape of bottom surface. The application of the modern IDE software will allow for using the obtained results in the marine hydraulic engineering at the design stage.