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In recent years, seaports have faced increasing pressure to transition towards a low-carbon and more sustainable energy model. In this context, the exploitation of the local wave energy resource may appear as a promising alternative. Therefore, the objective of this work is to present a methodology to select the best WEC-site combination to supply the energy demands of ports. To illustrate this methodology, the Port of Leixões (Portugal) is used as a case study. For the selection of wave energy sites in port areas, the methodology proposes a detailed spatial characterisation of both the wave resource and marine uses. For the area of study, having considered the main marine uses (sediment disposal, biodiversity, aquaculture, recreational and navigation), two exploitable wave energy sites (Areas I and II) with average annual energy resources of 24 and 17 kWm<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mo>−</mo><mn>1</mn></mrow></msup></semantics></math></inline-formula>, respectively, were found. Next, the methodology proposes a techno-economic optimisation of WECs, based on the local wave conditions of Areas I and II, to minimise their associated Levelised Cost of Energy (LCoE). The results obtained confirm the effectiveness of the methodology, with the novel oCECO device, appearing as the most feasible option (with an LCoE of EUR 387.6/MWh) to exploit the wave potential in the surrounding areas of the port.