The paper covers the research of microbiological destruction processes of petroleum origin pollutants in a shallow water taking into account a number of determining factors that affect the distribution of pollution in the researched water area: the oil fractional composition, the processes of evaporation, dissolution, biological oxidation of petro-hydrocarbons by microorganisms, as well as hydrodynamic and chemical-biological features of the water. A complex of interrelated spatially inhomogeneous mathematical models was proposed that allow researching the dynamics of microbiological destruction processes of petroleum hydrocarbons in shallow water. Schemes with weight taking into account the partial filling of computational cells of the simulated domain were developed at model discretization that made it possible to significantly increase the accuracy of calculations and reduce the calculation time. Based on a multiprocessor computer system, experimental software has been developed for predictive modeling of the ecological situation of shallow water in the event of accidental pollution by oil and other harmful substances during natural and technogenic challenges.