The two-dimensional plane water flow and water quality was developed by using the techniques of coordinate transformation, altating directions, staggered grid, linear recurrence, and implicit scheme in the study of large water body in lakes. The model was proved to be suitable for treating the irregular boundary and predicting quickly water flow and water quality. The application of the model to the Bosten Lake in Xinjiang Uygur Autonomous Region of China shows that it is reasonable and practicable.