Agricultural water use is increasing quickly with the rapid socioeconomic development observed in the Wuyuer River basin. Water withdrawal for agriculture over the past decade have seriously depleted the ecological water requirements in the basin and damaged the channel and downstream wetland ecosystems. Achieving sustainable development in the basin will require a balance between agricultural water exploitation and ecological water demands. In this paper, a reservoir and diversion engineering module was integrated with a dualistic distributed hydrological model (WEP model) to investigate the effects of agricultural water use on river discharge. Agricultural water shortages and yearly minimum river discharges between 2020 and 2050 under six agricultural water exploitation scenarios and one natural scenario were estimated based on the proposed model. The results showed that the dualistic hydrological process model was more suitable for basins with agricultural water resource exploitation and that the river discharge was significantly less than the natural discharge due to irrigation and reservoir filling, especially in drought years. Under the scenarios of high, middle and low water resource exploitation without ecological operations, agricultural development was unsustainable because of agricultural water shortages and ecological water scarcity. The evaluation of the guaranteed rates for the agricultural water supply and environmental flows showed that the low water resource exploitation scenario with ecological operations was the best option and that sustainable development could be achieved in the basin under this exploitation scenario in the future. However, implementing water management practices in the basin could result in certain economic losses. These losses could be offset by ecological protection funds for downstream wetlands. Overall, the model results could help to inform planning and investment decisions within the basin to improve the sustainable management of water resources.