Operational rules of managed river systems are often developed based on historical hydrology. This approach fails to consider alternative plausible hydrologic conditions that may occur in the future or have occurred in the past before records were taken. This paper aims to evaluate whether the operating rules for a managed river system under past hydrologic regimes will perform satisfactorily under an array of alternative stationary hydrologic conditions. We focus on a transboundary managed multi-reservoir river system in the Southeast US, Apalachicola-Chattahoochee-Flint Basin, which has a series of reservoirs managed for multiple purposes. We evaluated the response of this basin under the historical observations and 100 stochastic streamflow realizations of stationary hydrology. These scenarios were simulated by coupling a stochastic streamflow model with a river system model. We used these scenarios to evaluate the multi-reservoir system response of multiple metrics–urban water supply, overall water storage for required freshwater inflows, forest ecosystem water needs and hydropower generation. We found that the basin response and the current operation rules were generally less favorable under the revised hydrologic scenarios than historical hydrology. Low flows were predicted to be more persistent and frequent, thereby more severely endangering water supply and ecosystem health and the amount of hydropower generation was smaller. We suggest that, other managed basins that their operation rules were defined based solely on historical hydrology, should analyze the performance of management rules under a broader range of hydrologic conditions.