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Biodiversity conservation in economic areas like ports has recently become more important in the European Union due to a stricter interpretation of nature protection laws. In this study we develop a planning and design strategy—the ‘habitat backbone'—with which to support the long-term survival of pioneer species that occur in ports and have low dispersal abilities. For those species, long-term survival in port areas is uncertain because supply of their habitats (on vacant lots) is capricious and depends on land use dynamics. By gaining knowledge about spatial and temporal characteristics of these dynamics we were able to develop a solution to conserve such species. Our solution is based on the creation of permanent habitat—defined as a ‘backbone'—n (semi-) public land with an overall carrying capacity sufficient to support persistent populations. This best ensures long-term survival, and the backbone may also act as refugium. Satellite populations that emerge on adjacent vacant lots will thereby add to the persistence of the overall metapopulation. Management of permanent habitat is focused on retaining early-successional stages of vegetation. Implementing this strategy in the case of the natterjack toad in the Port of Antwerp taught us that realization of a habitat backbone is possible only if landowners, local governments and environmental NGOs cooperate. In the case at hand, such cooperation resulted in a plan that should ensure a coherent and persistent habitat network in which a chorus of some 1,400 natterjack toads could be accommodated—more than the number of toads currently observed.