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The 2009-2010 El Nino was accompanied by a severe drought strongly impacting Mexico as well as Central America, the Caribbean, and the southern USA. The present work aims at assessing how such a major climatic event impacted the hydrological typology of transitional waters in Terminos Lagoon, one of the largest shallow tropical lagoons fringing the Gulf of Mexico. Spatiotemporal inter-comparison of hydrological conditions was conducted by pairing a reference multiparametric dataset (14 hydrological parameters versus 34 sampling stations) averaged over the October 2008 to July 2010 period with each sampling occurrence dataset and running Principal Component Analyses (PCA), setting the reference-survey dataset as active variables and each sampling occurrence dataset as non-active (supplementary) variables. It revealed that the exceptional deficit in freshwater supply to the lagoon during the 2009-2010 El Nino drastically reduced hydrological diversity and lowered the trophic status of the lagoon. Short-term shifts in environmental status are common in transitional waters and responsible for temporary shifts in community structure but climate change projections show a significant long-term decrease in the freshwater discharge at the regional scale that will impact Terminos Lagoon as well as other coastal lagoons of Mexico and Central America. When combined with sea level rise, such a decrease will result in a long-term shift in hydrological conditions with a subsequent increase in salinity and a decrease in the diversity of environmental conditions affecting trophic status, will have a long-term impact on the biota.