It is difficult to simultaneously manage the dynamic demands for river water quality and quantity, and reconcile the contradiction between socio-economic and eco-environmental water consumption. As a solution, we proposed a three-tier model to optimize the distribution of river water resources. Using three constraint conditions, namely the ratio of wastewater to clean water, the eco-environmental water requirements of each node and the use of wetland projects, we determined various water quantity and quality allocation scenarios. We tested the model on the Qingyi River, and found that, for the recommended scenario that involved enhanced water-saving, a wastewater/clean water ratio and wetlands, more than 80% of the eco-environmental water requirements of each node except for the Luma section were achieved for each month. While the water quality in some individual river sections did not meet the standards for a few months of the year, the water quality of the remaining sections could be improved from class V, the current state, to class IV, and ammonia nitrogen and chemical oxygen demand (COD) standards could be achieved 82% and 96% of the time, respectively. These results show that the proposed model is effective and fit for purpose.