Abstract: Construction of small artificial lakes have affected the hydrodynamic characteristics, migration, diffusion and transformation processes of pollutants in the water network. Therefore, we constructed a aquatic ecological model of one-dimensional river network and two-dimensional shallow lake in this paper. The model included state variables, constants, diriven forces, processes, auxiliary variables and derivative variables. The measured data from Qingyi River Basin was used to verify the aquatic ecological model. The flow and water quality distribution in the lake under different water exchange frequency, water exchange modes namely constant flow rate and fluctuating flow rate mode were simulated in order to reveal the hydrodynamic characteristics and pollutants migration and transformation laws in the lake. Combining with the pollutant reduction with effluent quality, we proposed the optimal scheme for water network connection. The results show that using the regulation mode of combining circulation with water exchange, controlling the circulation flows of the lake group between 0.03 m3/s and 0.20 m3/s in Qingyi River Basin and changing water three times in March, July and November every year, the water network connection is the most effective.