A mathematical model of filtration consolidation of an inhomogeneous soil mass was formed taking into account the change in the size of the area during the compaction process. The inhomogeneity is considered as the presence of fine inclusions (geobarriers) the physical and mechanical characteristics of which differ from those of the main soil. From a mathematical viewpoint, the model is described by a one-phase Stefan problem that has a kinematic boundary condition on the upper moving boundary as its component. The purpose of the research is to find out the effect of fine inclusion on the dynamics of subsidence of the soil surface in the process of compaction. The change in the dimensions of the solution area is physically determined by the change in the volume of the pores of the porous medium in the process of dissipating excess pressure. If the permeability of the geobarrier is low, it affects the dynamics of consolidation processes and, accordingly, the magnitude of subsidence. Finite element solutions of the initial-boundary value problem for the nonlinear parabolic equation in the heterogeneous region with the conjugation condition of non-ideal contact were found. Numerical time discretization methods, a method for determining the change in the position of the upper boundary at discrete moments of time, and an algorithm for determining the physical and mechanical characteristics of a porous medium depending on the degree of consolidation are given. A number of test examples were considered, and the effect of a thin inclusion on the dynamics of the change in the position of the upper boundary of the problem solution area was investigated.