Through a nested suite of methods here we contrast the coexistence of different ecosystem states in a tropical coastal lagoon, the Laguna Larga, with increasing eutrophication stress between 2007 and 2009. Water temperature averaged 27.4°C in the lagoon and showed a slight positive trend during the study period. Salinity averaged 35.0±6.2, exhibiting high spatial and temporal variability, and also a slight positive trend in time. In contrast, dissolved oxygen showed a substantial decreasing trend (–0.83 ml L–1 y–1; –13.3% y–1) over the period, while nutrients increased dramatically, particularly total phosphorus (2.6 µM y–1), in both cases sustaining the progression of eutrophication in the lagoon during the three years we sampled. The Karydis nutrient load-based trophic index showed that the lagoon has a spatial pattern of increasing eutrophication from the sea and the outer sector (oligotrophic-mesotrophic) to the central (mesotrophic) and the inner sector (mesotrophic-eutrophic). Two ecosystem states were found within the lagoon. In the outer oligotrophic sector, the dominant primary producers were macroalgae, seagrasses and benthic diatoms, while mollusc assemblages were highly diverse. In the inner and central sectors (where trophic status increased toward the inner lagoon) a phytoplankton-dominated ecosystem was found where mollusc assemblages are less diverse. In spite of the progression of eutrophication in the lagoon, these two different ecosystems coexisted and remained unchanged during the study period. Apparently, the effect of water residence time, which increases dramatically toward the inner lagoon, dominated over that of nutrient loadings, which is relatively more homogeneously distributed along the lagoon. Therefore, we consider that actions that reduce the water residence time are likely the most effective management options for this and other similarly choked lagoons.