In recent years, the number of adverse and dangerous natural and anthropogenic phenomena has increased in coastal zones around the world. The development of mathematical modeling methods allows us to increase the accuracy of the study of hydrodynamic processes and the prediction of extreme events. This article discusses the application of the modified Upwind Leapfrog scheme to the numerical solution of hydrodynamics and convection–diffusion problems. To improve the accuracy of solving the tasks in the field of complex shapes, the method of filling cells is used. Numerical experiments have been carried out to simulate the flow of a viscous liquid and the transfer of substances using a linear combination of Upwind and Standard Leapfrog difference schemes. It is shown that the application of the methods proposed in the article allows us to reduce the approximation error in comparison with standard schemes in the case of large grid numbers of Péclet and to increase the smoothness of the solution accuracy at the boundary. The soil dumping and suspended matter propagation problems are solved using the developed schemes.