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Background: An important health issue in urban areas is how changes arising from the regeneration of city-areas affect social determinants of health and equity. This paper examines the impacts attributable to a new fish market and to delays in the regeneration of a port area in a deteriorated region of the Bay of Pasaia (Spain). Potential differential impacts on local residents and socially vulnerable groups were evaluated to determine health inequalities. Methods: An in-depth, prospective and concurrent Health-Impact-Assessment (HIA) focused on equity was conducted by the regional Public Health Department, following the Merseyside guidelines. Data from different sources was triangulated and impacts were identified using qualitative and quantitative methods. Results: The intervention area is characterised by poor social, environmental, and health indicators. The distinctness of the two projects generates contrasting health and inequality impacts: generally positive for the new fish market and negative for the port area. The former creates recreational spaces and improves urban quality and social cohesion. By contrast, inaction and stagnation of the project in the port area perpetuates deterioration, a lack of safety, and poor health, as well as increased social frustration. Conclusions: In addition to assessing the health impacts of both projects this HIA promoted intersectoral partnerships, boosted a holistic and positive view of health and incorporated health and equity into the political discourse. Community-level participatory action enabled public health institutions to respond to new urban planning challenges and responsibilities in a more democratic manner. This research was funded by the Basque Government's Department of Health (Ref. n. 2011111051).