Software has been developed in the C++ programming language using the MPI parallel programming technology, designed for mathematical modeling of the transport of substances in coastal systems.When calculating the dynamics of the spread of Pedal a pollutant, the decomposition of the computational domain was carried out to organize the computational process on a multiprocessor computer system K-60 in KIAM RAS.To solve the system of grid equations obtained as a result of the approximation ORG GREEN TEA of the problem, iterative methods were used, with a triangular preconditioner.