We conducted an extensive sampling program, using specific lagoon status over space as replicates of their evolution over time, and observed that open and closed lagoons are mutually exclusive alternative states of equilibrium, and ICOLLs are an intermediate or transition phase between them. The gradual regime shift of coastal lagoons, as they lose connectivity with the sea, changes the movement of resources and consumers, and the internal physico-chemical gradients that directly affected regional diversity, abundance and trophic status. Absence of barriers increased the diversity of nematode assemblages and the similarity between the fauna of more connected lagoons. Isolation increased the variation in species composition between lagoons and similarities within lagoons. As local processes within individual lagoons become increasingly more important as they lose connectivity, depending on the local stable state an alternative regional pattern of biodiversity may emerge.