In order to determine the possibility of using the method of mathematical modeling for making long-term forecasts of channel deformations of trunk line underwater crossing (TLUC) through water obstacles, a methodology for performing and analyzing the results of mathematical modeling of channel deformations in the TLUC zone across the Kuban River is considered. Within the framework of the work, the following tasks were solved: 1) the format and composition of the initial data necessary for mathematical modeling were determined; 2) the procedure for assigning the boundaries of the computational domain of the model was considered, the computational domain was broken down into the computational grid, the zoning of the computational domain was performed by the value of the roughness coefficient; 3) the analysis of the results of modeling the water flow was carried out without taking the bottom deformations into account, as well as modeling the bottom deformations, the specifics of the verification and calibration calculations were determined to build a reliable mathematical model; 4) considered the possibility of using the method of mathematical modeling to check the stability of the bottom in the area of TLUC in the presence of man-made dumping or protective structure. It has been established that modeling the flow hydraulics and structure of currents, making short-term forecasts of local high-altitude reshaping of the bottom, determining the tendencies of erosion and accumulation of sediments upstream and downstream of protective structures are applicable for predicting channel deformations in the zone of the TLUC. In all these cases, it is mandatory to have materials from engineering-hydro-meteorological and engineering-geological surveys in an amount sufficient to compile a reliable mathematical model.