Being one of the most important sources of water in the Jilin Province in China, the Yinma River Basin (YRB) is facing problems of water scarcity in low economic areas and low utilization in richer areas mainly caused by the irrational allocation of water, excessive pursuit of economic benefits, and neglect of environmental problems. Restricting watershed development involves potential decision-making risks. Some scholars have used the interval two-stage stochastic planning method to adjust water resource allocation in the Drinking Horse River Basin, but the method uses historical statistics for projection and does not take into account the ambiguity and uncertainty in real planning situations. Therefore, this study addresses the problems prevalent in the allocation of water resources in the YRB through optimization using stochastic programming methods, interval and two-stage, and introduces the fuzzy mathematical programming method, with the aim of coordinating the water balance of various water-consuming sectors in the YRB, so as to reconfigure the water allocation. The goal is to solve the existing problems of irrational water allocation, reduce system risks posed by excessive economic development, mitigate water shortages in the water-consuming sectors, and alleviate potential decision-making risks and vague uncertainties associated with the allocation of water resources. Additionally, optimization of the pollution-holding capacity improvement project was carried out. The interval fuzzy two-stage model simulation developed in this study shows that the distribution of water across the different administrative regions can be reduced by up to 30% compared with the original model, effectively reducing the problem of water wastage. Post-optimization, the impact of water shortage in the water resources allocation scheme is alleviated to a significant degree, and there is no water shortage in some areas. At the same time, the eco-environmental sector has gradually taken the leading role in the distribution of water reuse among the different water-consuming sectors. The pollution-holding capacity has been enhanced, and the discharge and river entry chemical oxygen demand (COD) and ammonia nitrogen, two typical pollutants, have been reduced. The membership interval in the interval fuzzy two-stage model reflects the relationship between the possible level of the target value and the risk level. This study provides a guideline for decision makers for balancing the relationship between benefits and risks and proposes a planning scheme that is more conducive to the development of the river basin.