Lagoons are a special type of transitional waters, as they occupy an important niche between land and sea, between the characteristics of a watershed and the open ocean. They have their own processes and are dependent on the processes of freshwater runoff, land, coast, and sea. However, they are also sites of significant urban and industrial development, including ports, aquaculture, and fishing. It is evident that lagoon researchers must align their work with the natural conditions to the real-world management, administration, and governance in these areas. We will increasingly need to address the eutrophication of coastal areas. Human development along the coast will not reduce the input of nutrients and organic matter that cause eutrophication. We need to explore effective management strategies that counteract the effects of eutrophication.