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This paper developed an interval multiobjective two-stage stochastic programming (IMO-TSP) model. The model integrated interval two-stage stochastic programming (ITSP), interval linear multiobjective programming (IMOP), and the analytic hierarchy process (AHP) method. The IMO-TSP model could not only address the conflicts of multiple objectives under uncertainty but could also obtain the optimal allocation results based on the water managers’ experience, knowledge, and local policies. In addition, a solution method was proposed to solve the IMO-TSP model by integrating the Zimmermann’s fuzzy method and the typical ITSP solution method. The developed model was applied to a real-world case for supporting the allocation of limited water resources to various water-use sectors. From the results analysis, the single objective model with a certain indicator can obtain the maximum value of that objective but can hardly take other significant factors into consideration. Conversely, the IMO-TSP model can effectively balance the three objectives of maximizing the system net benefit, minimizing the total COD discharge, and minimizing the water deficit by obtaining the best coordinated satisfaction. The obtained coordination satisfaction by the IMO-TSP model was [0.74, 0.83] in this study, which indicates that the results obtained by the developed model can allocate limited water resources to various water users with a high degree of coordination among the three objectives under different flow levels. The developed model can help the water managers of arid regions to develop the desired and reasonable water resources management policies under uncertainty.