Background: We studied the relationships between zooplankton distribution and environmental and trophic factors (abiotic variables, nutrients, bacterial biomass, and chlorophyll pigments) from three sampling surveys carried out during the three hydrological seasons (rainy, dry, and norte) in a tropical coastal lagoon connected to the sea. Results: Twenty eight (28) of the 54 taxa recorded were identified to species level, of which 3 genera of Cladocera were observed for the first time in the lagoon. Season-specific differences were highly significant. The overall zooplankton abundance was significantly higher during the dry season (157,000 ind.m −3 ) than those during the rainy and norte surveys (means of 11,600 and 16,700 ind.m −3 respectively). Copepoda (mostly nauplii) was the most abundant group (>83%) of total zooplankton abundance. Conclusions: Multivariate (coinertia) and multilinear regression analyses showed that transparency, salinity, temperature, pH, and food availability (Chl a, b, and c) were the main determinants of zooplankton abundance, composition, and diversity, explaining the seasonal differences. The relatively low zooplankton density in the lagoon compared to other eutrophic lagoons is attributed to the combined effects of high water exchanges, low depth, and high transparency, which favor instability and vulnerability to UV effects and/or to visual predation.

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