Intermittently open/closed lagoons are particularly important in the understanding of biological and physico-chemical shifts between coastal lagoons/lakes. This is because, in the short-term, changes in the connectivity of ICOLLs leads to drastic environmental changes , shifting between the lacustrine or the lagoonar equilibrium state. The sampled ICOLLs in this study were not in the same status of closure (3 were closed and 2 were open) and our expectations were that nematode assemblages of the ICOLLs would be grouped with the closed or the open lagoon samples depending on their inlet state. Instead, we found that ICOLLs univariate and multivariate descriptors of the nematodes assemblages had an intermediate structure between lagoons and coastal lakes. ICOLLs are typically characterized by low freshwater inflow, which leads to sand berm formation across the mouth, preventing mixing with ocean water . Besides, high intra and inter-annual variability in rainfalls and discharges are typical of ICOLLs . A possible mechanistic explanation for the transitional structure of the nematode assemblages is the intermediate pattern of isolation compared to lagoons and coastal lakes. Increasing isolation from open ocean conditions also alters the structure of foraminiferans and macrobenthic assemblages, leading to a decrease in diversity and changes of species . The higher diversity of nematode assemblages in brackish water compared to freshwater reflects both the input of marine species and the presence of strong environmental gradients and higher environmental heterogeneity. Overall freshwater nematode communities are impoverished when compared to marine and brackish systems . Regarding nematode abundance, higher values in open lagoons and ICOLLs probably reflects the amount of organic matter. Although just marginally significant, closed lagoons had lower TOC than ICOLL and open ones. Moreover, TOC was significantly higher in the outer portion of open lagoons and ICOLLs, as observed for nematode abundances, giving support to the hypothesis that TOC plays a significant role in nematode abundances .