Coastal lagoons are by nature complex and fragile systems characterized by large fluctuations in their physical and chemical parameters. This is primarily due to their location between land and open sea, which makes their equilibrium strongly influenced by the quality of inland waters flowing into them. Over the last decades, they have also become an extremely valuable economic resource. The increase in value is mainly concerned with the enormous potential of these sites for residential, tourism and economic (shellfish/fish farming) development. However, concepts like sustainable use of natural resources and sustainable coastal development are often disregarded. Overcrowding, degradation of water quality, resource exhaustion, conflicting use of resources, multiple and uncoordinated ecosystem modifications (e.g., structural changes in lagoon topography, artificial increase of the number of sea connections, changes in bathymetry, etc.) undertaken with only limited sectorial objectives in mind, are some of the current issues associated with coastal areas, and contribute to the decrease of their economic potential. Hence, it is apparent that decisions need to be made in an integrated way by taking into account economic, environmental, social, and political aspects.