Recent droughts have caused a crisis in the water supply procedure, because as available water resources become more limited, the imbalance between the growing water demand and water supply in different sectors leads to unsustainability in the system. Thus, this study proposes a dynamic model to optimize water supply system under different scenarios aimed at improving sustainability of system. In fact, due to the negative impacts of the water crisis, the sustainability of the dynamic water supply system is evaluated and optimized according to the performance indicators of the system. Also, to investigate the proposed model, a real case study of the Sistan basin in Iran over ten years period is conducted. Based on the model, different management insights along with the scenario analysis are considered in order to assess the sustainability of system in more detail. According to the final output, the highest level of sustainability is related to the domestic sector because it has higher reliability and less vulnerability than other sectors.