A water quality systematical filter model and its algorithm in a shallow lake have been established. On the basis of relative stability of flow field, cunsidering 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 to solve differential equation. BOD and COD concentrations during 1988 in Dianchi Lake iji Yunnan Province have been simulated. The computed results by using this model are ia good agreement with the observed field data.