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Increasing water demand aggravates water scarcity in water-scarce regions (e.g., India, Pakistan, and China), where uneven precipitation increases the risk of maintaining sustainable eco-economic development. Ignoring precipitation's effects leads to misguided policy recommendations that either deplete or underuse basin water resources. Therefore, this paper highlights the concept of uneven precipitation and uncertain stream inflow based on scenario analysis. Within a river basin, the regional authority and subarea managers both have water allocation and reallocation privileges. Motivated by sustainable development of water resource management systems, we argue that regional authorities should focus on alleviating the contradiction between supply and demand, and then seeking an optimum allocation strategy to ensure societal and economic benefits for its subareas, from which the subareas cart provide reasonable reaction strategies. Authorities dominate water transactions between subareas involved in water rights distribution. This paper proposes a multi-objective multistage Stackelberg-Nash-Cournot (m(2)SNC) game model to cope with conflicts between regional authorities and subarea managers concerning multiple activities. An interactive-dynamic-programming-based genetic algorithm (IDP-GA) is designed to simulate the policies needed for the optimum allocation of water resources under various climate scenarios. The significant stress caused by unsustainable water resource allocation has been a perplexing problem for Sancha Lake, an important area in the southeast basin of the Dujiangyan Irrigation System in China. To identify the tradeoffs among stakeholders, we apply the proposed model to this basin. To gain further insight into climate change and water usage sustainability, we simulate the varying spatial and seasonal distribution of stream inflow based on historical climate data and propose different water management strategies for normal, slight drought, moderate drought, and serious drought conditions. This creates an emergency response cooperative mechanism based on different climate scenarios for developing countries that need to cope with water deficiency and uncertain situations.