Zayandehrud basin contains important water transfer projects, like transfer from Kuhrang springs to the basin and transport from basin to the Yazd and Kashan cities. Assessment of the impacts of these projects (and guidelines for alleviating these impacts) on water supply capability of Zayandehrud hydro-system, especially under long-term hydrologic uncertainties, is a very important issue for water sector decision makers and waterbasin stakeholders. In this research, the impacts of drought and future development of water transport projects is analyzed by a non-linear long-term optimization model for a 10-year horizon. Results showed that in normal (and transfer development scenario) conditions, on average 43% and 57% withdrawal from river and groundwater, respectively, leads to the least shortage in water supply to demands. Besides, Zayandehrud hydro-system operation can be managed in the case of a severe drought with 40% reduction in river flow that only 6% reduction occurs in water supply in comparison with normal condition. Analysis of the results showed the robustness of multi-period optimization model in minimizing the impacts of drought and water transfer development by making use of the spatial and temporal potentials of Zayandehrud hydro-system.