The water quality systematical filter model and its algorithm in shallow lake have been established in this paper.On the basis of relative stability of flow field, considering the disturbances of model error and observation error, the systematical state equation and observation equation can be gained by dividing the lake into calculated units.The model has properties of continuous simulation and real-time prediction by employing GILL method of solve differential equation. BOD and COD concentrations during 1988 in the Dianchi Lake in Yunnan Province has been simulated. The computed results by using this model are in good agreement with observational field data.