Optimizing water allocations for the agricultural sector, the main water consumer, at the beginning of a period of drought is essential. However, long-term inflow forecasting, with its high uncertainty, is a necessary component of the allocation process. This paper presents a methodology that combines this uncertainty with economic factors to determine water allocation. The following models were developed and linked: optimization of agricultural water allocation under water scarcity, long-term flow forecast and quantification of forecast uncertainties. The approach coordinates economic values of water with system operational requirements. The Zayandeh Rud dam and irrigation system was selected to explore the methodology of this research.