Coastal lagoons are extremely rich, diverse, and dynamic but very fragile ecosystems subject to anthropogenic pressures. A joint France–Mexico biogeochemical study was conducted in the Términos Lagoon under severe drought related to an El Niño Modoki episode. In short, the water column of the Términos Lagoon functioned as a nitrogen sink, but variation in mineral stoichiometry across the lagoon mainly accounted for the heterogeneity in microbial distribution and activity.