Our results further showed that similarities of the nematode assemblages within and between lagoons also change according to the stable state. While habitat connection and faunal exchange by open inlets increased similarity between more connected lagoons, with variations in the composition controlled by gradients, isolation increased variability of nematode assemblages between closed lagoons. At the same time, internal variability was higher within open lagoons than in closed lagoons, with ICOLL again assuming an intermediate position. This pattern may emerge as a result of the connectivity that modulates the degree to which the inlet state facilitates or impedes the exchange of matter, energy and specimens among landscape elements. Besides, differences in structural connectivity can lead to internal homogeneity or strong physico-chemical gradients that directly affect species composition.