Rapid urbanization and population growth have resulted in serious water shortage and pollution of the aquatic environment, which are important reasons for the complex increase in environmental deterioration in the region. This study examines the environmental consequences and economic impacts of water resource shortages under variant economic policies; however, this requires complex models that jointly consider variant agents and sectors within a systems perspective. Thus, we propose a complex system model that couples multi-agent based models (ABM) and system dynamics (SD) models to simulate the impact of alternative economic policies on water use and pricing. Moreover, this model took the constraint of the local water resources carrying capacity into consideration. Results show that to achieve the 13th Five Year Plan targets in Dianchi, water prices for local residents and industries should rise to 3.23 and 4.99 CNY/m3, respectively. The corresponding sewage treatment fees for residents and industries should rise to 1.50 and 2.25 CNY/m3, respectively, assuming comprehensive adjustment of industrial structure and policy. At the same time, the local government should exercise fine-scale economic policy combined with emission fees assessed for those exceeding a standard, and collect fines imposed as punishment for enterprises that exceed emission standards. When fines reach 500,000 CNY, the total number of enterprises that exceed emission standards in the basin can be controlled within 1%. Moreover, it is suggested that the volume of water diversion in Dianchi should be appropriately reduced to 3.06×108m3. The reduced expense of water diversion should provide funds to use for the construction of recycled water facilities. Then the local rise in the rate of use of recycled water should reach 33%, and 1.4 CNY/m3 for the price of recycled water could be provided to ensure the sustainable utilization of local water resources.