In this study, a multistage scenario-based interval-stochastic programming (MSISP) method is developed for water-resources allocation under uncertainty. MSISP improves upon the existing multistage optimization methods with advantages in uncertainty reflection, dynamics facilitation, and risk analysis. It can directly handle uncertainties presented as both interval numbers and probability distributions, and can support the assessment of the reliability of satisfying (or the risk of violating) system constraints within a multistage context. It can also reflect the dynamics of system uncertainties and decision processes under a representative set of scenarios. The developed MSISP method is then applied to a case of water resources management planning within a multi-reservoir system associated with joint probabilities. A range of violation levels for capacity and environment constraints are analyzed under uncertainty. Solutions associated different risk levels of constraint violation have been obtained. They can be used for generating decision alternatives and thus help water managers to identify desired policies under various economic, environmental and system-reliability conditions. Besides, sensitivity analyses demonstrate that the violation of the environmental constraint has a significant effect on the system benefit.