The present work aims at presenting an approach on implementing appropriate mitigation measures for the upgrade of rubble mound breakwaters protecting harbors and/or marinas against increasing future marine hazards and related escalating exposure to downtime risks. This approach is based on the reliability analysis of the studied structure coupled with economic optimization techniques. It includes the construction of probability distribution functions for all the stochastic variables of the marine climate (waves, storm surges, and sea level rise) for present and future conditions, the suggestion of different mitigation options for upgrading, the construction of a fault tree providing a logical succession of all events that lead to port downtime for each alternative mitigation option, and conclusively, the testing of a large number of possible alternative geometries for each option. A single solution is selected from the total sample of acceptable geometries for each upgrading concept that satisfy a probabilistic constraint in order to minimize the total costs of protection. The upgrading options considered in the present work include the construction or enhancement of a crown wall on the breakwater crest, the addition of the third layer of rocks above the primary armor layer of the breakwater (combined with crest elements), the attachment of a berm on the primary armor layer, and the construction of a detached low-crested structure in front of the breakwater. The proposed methodology is applied to an indicative rubble mound breakwater with an existing superstructure. The construction of a berm on the existing primary armor layer of the studied breakwater (port of Deauville, France), seems to be advantageous in terms of optimized total costs compared to other mitigation options.