The Qinling Mountains are located in a transition zone between (semi)-arid regions in north China and humid regions in south China. The water resource and water ecology of regional rivers are strongly affected by climate change and human activity. In this paper, the stochastic simulation of river water regulation was performed and an optimal water regulation scheme of rubber dam projects was developed by establishing a multi-objective stochastic constraint water regulation model of rubber dam projects based on the coupling of a distributed hydrological model and a water balance model. Results show that a ∼40% reduction of water occurred in the lower river channel due to the operation of water supply project in the upper reach and impoundment by rubber dam projects in the lower reaches. This water reduction was associated with decreased water environment self-purification capacity and serious deterioration of water quality for smaller ecological basic flow and mean flow velocity. By establishing a multi-objective stochastic constraint programming model, the average velocity and the ecological basic flow at different adjusting heights of rubber dams are determined. The regulation scheme of rubber dam projects we propose in this paper may optimize the current river water management strategies and help to improve the river water quality environment in urban rivers.