Coastal lagoons are subjected to strong anthropogenic pressures mainly from urban, agricultural, and industrial effluents and domestic sewage, but also due to the intensive shellfish farming (for a recent review, see Zaldívar, Cardoso, et al. 2008). For example, the Thau lagoon in southern France is an important site for oysters (Crassostrea gigas) and mussels (Mytilus galloprovincialis) farming (Bacher et al. 1995); the Adriatic lagoons in northern Italy—namely the Venice, Scardovari, and Sacca di Goro lagoons—on average attained a production of around 60,000 t yr−1 of the Manila clams, Ruditapes philippinarum (Solidoro et al. 2000). The combination of all these pressures calls for an integrated management that considers lagoon hydrodynamics, ecology, nutrient cycles, river runoff influence, shellfish farming, macroalgal blooms, and sediments, as well as the socioeconomical implications of different possible management strategies. Historically, coastal lagoons have undergone multiple and uncoordinated modifications undertaken with only limited sectorial objectives. For example, land-use modifications in the watershed affect the nutrient loadings to the lagoon, and modifications in lagoon bathymetry by dredging change the hydrodynamics. All these factors are responsible for community shifts, and trophic status changes up to eutrophic and dystrophic conditions are achieved, with macroalgal blooms (Viaroli et al. 2008), oxygen depletion, and sulphides production mainly in summer (Viaroli et al. 1995; Chapelle et al. 2001; Marinov et al. 2008; Giordani, Azzoni, et al. 2008).