Using particular lagoon status over space as replicates of their evolution over time, we observed that open and closed lagoons are mutually exclusive alternative states of equilibrium, and that ICOLLs are an intermediate or transition phase between them. The gradient in the structural connectivity between lagoons and the sea, due to their regime shifts, changes the movement of resources and consumers, and the internal physico-chemical gradients that directly affected the regional species diversity, abundance and trophic status. Whereas the lack of barriers and the fauna movements through the inlets increased similarity between the more connected lagoons, isolation increased variation in the composition of nematode assemblages with species losses and decrease of trophic diversity between closed lagoons.