Abstract: The transportation and diffusion process of pollutants in the water current is affected by the water temperature, local flow velocity and direction, and watercourse forms, etc. Therefore, the concentration of pollutant at any point of the downstream of discharge outlet is a fluctuating variable rather than a constant. Apparently, certainty models are not suitable for precisely describing the variation and the fluctuation. The stochastic model is thus needed. To precisely describe and simulate the trend of water quality variation of the Yangtze River mainstream after construction of the Three Gorges Reservoir, a two-dimensional stochastic prediction model of water quality is set up.