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Excess supply of nutrients of anthropogenic origin is one of the main drivers of global change that is affecting the ecological function and provision of ecosystem services by coastal wetlands. This study examines the response of a subtropical semi-arid coastal lagoon to anthropogenic nutrient input, through the use and comparison of eutrophication indices and models, and compares the usefulness of such methods to identify eutrophication symptoms. The Lobos Lagoon is located on the eastern coast of the Gulf of California and receives agricultural and urban wastewater discharges. To identify potential eutrophication symptoms, the Trophic IndeX (TRIX), the Arid Zone Coastal Water Quality Index (AZCI) along with the Assessment of Estuarine Trophic Status (ASSETS) model were used. Lobos Lagoon was found to have good environmental condition; however eutrophication symptoms were identified in the zone where untreated urban and agricultural wastewaters are discharged. Results obtained using the three methods were consistent and, thus, their performance can be considered as good and complementary, and can be used to evaluate the extent of eutrophication in subtropical semi-arid coastal lagoons.