Coastal lagoon ecosystems are dynamic and open systems, dominated and subsidized by physical energies, and characterized by particular features (such as shallowness, presence of physical and ecological boundaries, and isolation) that distinguish them from other marine ecosystems.1 Shallowness usually provides a lighted bottom, and the wind affects the entire water column, promoting resuspension of materials, nutrients, and small organisms from the sediment to the surface layer. The large number of boundaries (between water and sediment, pelagic and benthic communities, and among lagoon, marine, freshwater, and terrestrial systems and with the atmosphere) involve the existence of intense gradients and, consequently, a high potential to do work.1 (Figure 5.1). Because of that, coastal lagoons are usually among the marine habitats with the highest biological productivity.2 Nutrient input from both run-off and irrigated land waters and from currents through tidal channels contribute to increase the primary productivity affecting the structure of the communities. On the one hand, due to their relatively high degree of isolation, outlets usually have a total surface of less than 20% of the barrier closing the lagoon,3 and the water exchange between lagoons and the open sea is limited, resulting in a series of physical, chemical, and hydrodynamic boundaries.4 On the other hand, the generated environmental stress regulates the structure of biological assemblages and leads to complex interactions among physical (light, temperature, mixing, flow), chemical (organic and inorganic carbon, oxygen, nutrients), and biological parameters and processes (nutrients uptake, predation, competition).