In this article, we provide a general overview of eutrophication in aquatic ecosystems, with a focus on the Mediterranean Sea and two Sardinian lagoons (western Mediterranean Sea, Italy), as case studies. In the Cabras Lagoon, we assessed the nutrient budget and fluxes using the biogeochemical Land–Ocean Interaction Coastal Zone model. High nutrient and chlorophyll‐
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concentrations indicated eutrophic conditions, summer being the most critical season as related to the decrease in riverine water supply, the increase in water evaporation and a concurrent isolation of the lagoon from the adjacent sea. In the Calich Lagoon, the eutrophic conditions, assessed during 2008–2015, seemed to be attenuated by a good water exchange with the sea, yet potential harmful phytoplankton species were found. Overall, the present study shows how Mediterranean coastal lagoons are strongly influenced by both terrestrial and marine ecosystems. Eutrophication is one of the main forms of environmental degradation of aquatic ecosystems, and in coastal lagoons, this is the consequence of multiple pressures, which have led to significant losses of major ecosystem goods and services, such as aquaculture, fishery, and tourism. Good practices and landscape management are urgently needed to prevent further deterioration of these sensible ecosystems.