Based on biochemical kinetics, a stochastic model to characterize wastewater treatment plants and dynamics of river water quality under the influence of random fluctuations is proposed in this paper. This model describes the interaction between dissolved oxygen (DO) and biochemical oxygen demand (BOD), and is in the form of stochastic differential equations driven by multiplicative Gaussian noises. The stochastic persistence problem for the model of the system is analysed. Further, a numerical simulation of the stationary probability distributions of BOD and OD by approximations of the stochastic process solution is presented. These results have implications for the prediction and control of pollutants.