An analysis for the impact on seagrass ecosystems of the eutrophic conditions recently reported for the Mexican Caribbean revealed large structural, floristic and community transformations over the last 20 years, but no adverse effects rather photosynthesis stimulation and increases in biomass, leaf area and species diversity. This contrasts with the declining global seagrass trend and the severe deterioration widely documented for adjacent coral reefs. Six meadow’ types and three community phase shifts were identified from oligotrophic conditions until a functional optimum was achieved and slightly surpassed in the northern region. Differences in the minimum light requirements and species’ plasticity for expanding the size of the photosynthetic light collector, explained germane interactions among species and early community transformations in response to habitat fertilisation. Understanding when ecosystem functional optima occur and community transformations beyond that optimality initiate will enable early detection of habitat deterioration (here, eutrophication) and appropriate and timely conservation actions.