In this study, an interval-stochastic fractile optimization (ISFO) model is advanced for developing optimal water-resources management strategies under multiple uncertainties. The ISFO model can not only handle uncertainties presented in terms of probability distributions and intervals with possibility distribution boundary, but also quantify subjective information (i.e., expected system benefit preference and risk-averse attitude) from different decision makers. The ISFO model is then applied to a real case of water-resources systems planning in Kaidu-kongque watershed, China, and a number of scenarios with different ecological water-allocation policies under varied p-necessity fractiles are analyzed. Results indicate that different policies for ecological water allocation can lead to varied water supplies, economic penalties, and system benefits. The solutions obtained can help decision makers identify optimized water-allocation alternatives, alleviate the water supply-demand conflict, and achieve socioeconomic and ecological sustainability, particularly when limited water resources are available for multiple competing users.