Natural and gradual shifts from lagoons to lakes are long-term processes that result from large-scale (e.g. sea-level and climate changes) and local processes (e.g. sediment supply, alongshore drift, coastal morphology) . The impoverishment of the nematode assemblages and the substitution of brackish water species by freshwater species also promotes a change in the trophic status of the benthic system and a significant decrease of trophic diversity. The dominant genera of closed lagoons Semitobrilus and Trischistoma are predators, while the genera Desmodora and Theristus are, respectively, epigrowth and non-selective deposit feeders . These findings indicate that the availability of trophic resources is strongly affected by shifts from lagoons to lakes, resulting in loss of functional diversity. Similar result was also observed for meiofauna in hard-bottom macroalgal meadow/barren regime shift . Besides, natural shifts may also interact with human interventions, increasing the speed of the shift and changing the dynamics of coastal lagoon evolution . Our results from the large-scale sampling program showed that as lagoons lose connectivity, gradually shifting the state, local processes within individual ICOLLs and particularly within lakes become increasingly more important factors in the structuring of these communities than differences in large scale process (such as geomorphology or biogeography). The main implication of these findings is that depending on the local stable state we may end up with alternative regional pattern of biodiversity.