Open lagoons are characterized by a wide spatio/temporal range in environmental conditions (e.g., salinity, temperature, oxygen), biological productivity and movement of resources and consumers with other adjacent marine areas . In contrast, coastal lakes are largely more homogeneous in their environmental conditions than open lagoons. Intermittently open/closed lagoons and lakes (ICOLL) show dramatic environmental changes over a short period of time, especially concerning hydrodynamics, salinity gradient, sediment composition and concentration of organic matter . This shift from a completely open coastal lagoon to a coastal lake causes abrupt changes in the biota  as expected by the alternative stable state model  (Fig 1B dashed line). The environmental shift might be induced by natural processes over geological scales, or by anthropogenic activities at the ecological scale, such as hydrological management , artificially connecting coastal lakes to the sea  or modifications as a result of climate change .