According to the water environmental governance for tidal lakes, a water ecology numerical model is developed based on the two-dimensional shallow water equations and convection-diffusion equation. The proposed model considers eight water quality indices, including dissolved oxygen (DO), ammonia nitrogen (NH3-N), nitrate nitrogen (NO3-N), organic nitrogen (ON), inorganic phosphorus (OPO4), organic phosphorus (OP), carbon biochemical oxygen demand (CBOD), and chlorophyll-a. The interactions of the eight water quality indices are modeled by four subsystems of the dissolved oxygen balance, nitrogen cycle, phosphorus cycle, and phytoplankton dynamics. The proposed model is applied to a tidal lake in the Pearl River Delta, and the spatial and temporal distribution of the chlorophyll-a under different scheme of water replacement is simulated, which gives the data support for water replacement scheme optimization. Results show that the proposed method can provide evidence for the control of eutrophication in tidal lakes.