The Valli di Comacchio are a large (115 km2) complex of shallow-water (with depth ranging from 0.5-1.5 m) brackish lagoons located in the southernmost part of the Po River deltaic area (Figure 1). The Valli are, nowadays, constituted by three main basins, i.e. Valle Magnavacca, Valle Fossa di Porto and Valle Campo. This semi-enclosed lagoonal complex is almost completely surrounded by earthen dikes, and separated by the sea by the highly anthropogenically impacted, 2.5 km-wide Spina spit. The Valli are connected with the Adriatic Sea by three marine channels, Portocanale, Logonovo and Gobbino, but since the latter is impounded, major water exchange with the sea occurs only through the firsts two channels. The former receives also nutrient-enriched continental water from Valle Fattibello. Water exchange with the sea is both tidal and man-regulated. Moreover, from February to May, large amounts of freshwater are conveyed through the Reno river through two dams in the southermost parts of Valle Magnavacca and Valle Fossa di Porto. Due to the shallowness of the basins and their limited water renewal, salinity (annual range: 24-38 psu) is mostly influenced by meteorological events, such as evaporation and occasional heavy rainstorms. The bottoms of the Valli are typically muddy, but sparsely vegetated meadows of the seagrass Ruppia cirrhosa occur in the southern parts of the Valli Magnavacca and Fossa di Porto. These meadows are the remnants of the larger macrophytic coverage that characterized the bottom of the Valli in the early 1970s