This paper applies a multi-objective evolutionary algorithm, the non-dominated sorting genetic algorithm (NSGA-II), to examine the operations of a multi-reservoir system in Taiwan. The Feitsui and Shihmen reservoirs are the most important water supply reservoirs in Northern Taiwan supplying the domestic and industrial water supply needs for over 7 million residents. A daily operational simulation model is developed to guide the releases of the reservoir system and then to calculate the shortage indices (SI) of both reservoirs over a long-term simulation period. The NSGA-II is used to minimize the SI values through identification of optimal joint operating strategies. Based on a 49 year data set, we demonstrate that better operational strategies would reduce shortage indices for both reservoirs. The results indicate that the NSGA-II provides a promising approach. The pareto-front optimal solutions identified operational compromises for the two reservoirs that would be expected to improve joint operations.