Most port cities have a long history of investment in the waterfront, adapting these spaces to improve the quality of life of its inhabitants and increase the tourist interest of the city, in a 50-year process of waterfront regeneration that started in the late 1960s. Even though one of the drivers of development in today’s port cities continues to be the transfer of knowledge and experiences between different cases, not all these cities have achieved their goals, nor have all done so in a sustainable way. This article exposes a new methodology, motivated by the need to carry out a comparative study of good practices of port–city integration for twelve specific cases. To enable a comparison of intangible realities such as port–city integration, it is mandatory to have a common benchmark to quantify features of cities from different cases. The 3DPortCityMeasure methodology is intended to provide a framework for analysing port-city integration, with results that supply an immediate understanding of each case. This tool enables direct comparative evaluation and provides support for land use planning and urban design approaches. The results show that the proposed approach for measuring intangible factors in the field of the port–city relationship is a very useful tool, novel in this discipline, and fully applicable to other cases and other urban issues.