We present the research on microbiological destruction of oil pollution in shallow water. In order to conduct the research, we use a multiprocessor computer system with distributed memory. The research takes into account the oil fractional composition as well as hydrodynamic and chemical-biological features of water. In order to simulate the dynamics of hydrocarbon microbiological degradation in the Azov Sea, we propose the complex of interrelated precision models. For model discretization, we use the space splitting schemes taking into account the partial filling cells of computational domain. Therefore, the computational accuracy significantly increases, while the computational time decreases. On supercomputer, we implement an experimental software for predictive modelling the ecological situation under oil and other pollution conditioned by natural and industrial challenges in shallow water.