A mathematical model was developed to numerically study the process of fluid and gas filtration in three-layer interacting pressure porous formations. It is based on the reviews related to the mathematical modeling developed in recent years; it describes a system of partial differential equations with boundary and initial conditions and a conservative numerical algorithm for conducting a computational experiment (CE) on a computer. In this article, to analyze and make managerial decisions, the results of numerical calculations are presented in the form of graphical objects, which can be used to propose schemes for the location and capacity of vertical drainage wells to protect irrigated and non-irrigated areas from flooding. Using the proposed mathematical tool, it is possible to obtain the predicted groundwater levels of any area for the required period of time, taking into account some factors, such as the inhomogeneity of the reservoir in a plan, the slope of the confining layer, and other hydrogeological, hydro-technical, and natural conditions, or to calculate the thickness and the optimal location of vertical drainage wells to protect the territory, and to develop oil and gas fields and increase their oil and gas recovery. Analysis of the results of a numerical study of the process made it possible to establish the degrees of influence of the elastic filtration regime in a weakly permeable layer on the overflow into adjacent layers.