The methodology for port management in this study takes into account the stochastic nature of climate as well as of use and exploitation agents. It provides a probabilistic characterization of the performance of different alternatives in terms of a set of indicators that reflect the potential benefits for different interest groups. The joint distribution functions thus obtained for a set of pre-defined management alternatives are used to compare strategies and to make decisions, based on stochastic multi-criteria analysis. This method, which also addresses the uncertainty of decision-maker preferences, ranked the strategies, and at the same time, specified the typical decision-maker preferences for each strategy. In the analysis of a hypothetical port, four alternatives were designed as solutions for port congestion. The criteria selected were the service quality provided to vessels, the total goods handled and the profits accrued by the Port Authority. The criteria measuring the performance of each strategy were statistically analyzed first. Then, assuming the uniform distribution of decision-maker preferences, the alternatives were ranked, and the relative importance of each criterion in the decision-making process was obtained.