Coastal habitats provide a variety of benefits for citizens living in littoral countries. The economic value of changes in coastal habitats in the context of the implementation of the Baltic Sea Action Plan, targeting good ecological status by 2021, in two coastal sites was estimated using the choice experiment method. The selected aspects of marine ecosystem were described in conjunction with ecological changes modeled within the Finnish-Swedish archipelago and the Lithuanian coast. The benefits for Finns, Swedes, and Lithuanians for changes in the adjacent coastal site were estimated with the conditional logit and random parameters logit models accounting for preference heterogeneity. The willingness to pay estimates for healthy perennial vegetation, protection of currently pristine areas, and size of fish stocks differed significantly between populations. The transfer errors ranging from 40%, when transferring the estimates for the same coastal site between populations, to 400%, when transferring between both sites and populations, underline careful consideration in value transfers.