A habitat transition model, based on the correlation between individual habitats and micro-elevation intervals, showed substantial changes in the future spatial distributions of coastal habitats. The research was performed within two protected areas in Slovenia: Sečovlje Salina Nature Park and Škocjan Inlet Nature Reserve. Shifts between habitats will occur, but a general decline of 42 % for all Natura 2000 habitats is projected by 2060, according to local or global (IPCC AR4) sea level rise predictions. Three different countermeasures for the long-term conservation of targeted habitat types were proposed. The most "natural" is displacement of coastal habitats using buffer zones (1) were available. Another solution is construction of artificial islets, made of locally dredged material (2); a feasible solution in both protected areas. Twenty-two islets and a dried salt pan zone at the desired elevations suitable for those habitats that have been projected to decease in area would offer an additional 10 ha in the Sečovlje Salina. Twenty-one islets and two peninsulas at two different micro-altitudes would ensure the survival of 13 ha of three different habitats. In the area of Sečovlje Salina, abandoned salt pans could be terrestrialized by using permanent, artificial sea barriers, in a manner close to poldering (3). By using this countermeasure, another 32 ha of targeted habitat could be preserved. It can be concluded that, for each coastal area, where wetland habitats will shrink, strategic plans involving any of the three solutions should be prepared well in advance. The specific examples provided might facilitate adaptive management of coastal wetlands in general.