The paper deals with the mathematical models, algorithms and software for mathematical modeling of coastal systems’ water pollution spreading dynamics under various unfavorable phenomena of natural and artificial genesis, developed for high-performance cluster systems. Methods for partitioning the computational domain for solving diffusion-convection problems have been developed, which allow for efficient parallelization of a computationally complex modeling problem, taking into account the architecture of the multiprocessor system used. The developed mathematical models are based on high-precision models of hydrophysics and hydrobiology and take into account the peculiarities of water systems in the south of the Rostov region, as well as factors of hydrobiological dynamics such as microturbulent diffusion and advective transport in various directions, mechanisms of primary and secondary pollution of coastal systems, taking into account currents. The paper presents algorithms for solving a simulated problem based on MPI parallelization technology, as well as based on mixed MPI + OpenMP technology. Numerical experiments have been carried out and the two technologies efficiency comparison has been made in the conditions of computing cluster used.