Zooplankton constitutes a sensitive tool for monitoring environmental changes in coastal lagoons; however, the available information on zooplankton communities is not sufficient to optimize their rational management. The relationships between zooplankton distribution and environmental factors were studied in a tropical lagoon to test whether the indicator properties of zooplankton assemblages could be used to monitor water quality, in a context of expected eutrophication provoked by an increasing anthropogenic activity. Twenty-one (21) stations were sampled monthly from January to December 2004. The community was composed of 65 taxa including Copepoda, Rotifera, and Cladocera. Copepoda was the most abundant group (81% of total numbers). The main zooplankton species were Oithona brevicornis, Acartia clausi, and Brachionus plicatilis. The highest zooplankton abundance (171–175 ind. l−1) was recorded during the long, dry season (February–April) and the lowest (40–45 ind. l−1) during the rainy and the flood periods (June–July). At a spatial level, the lowest abundance was observed in the estuarine zone. During the dry seasons (December–April and August–September), marine zooplankton taxa were abundant near the channel of Grand-Lahou, and brackish water taxa dominated in the other sites. Multivariate analyses (Co-inertia) showed that the composition of zooplanktonic communities and their spatio-temporal variations were mainly controlled by salinity variations closely linked to the climatic and hydrological context. The role of the trophic state on zooplankton communities could not be clearly evidenced. Our results and a comparison with previous studies in the neighboring, highly polluted Ebrie Lagoon suggest that the ratio between Oithona and Acartia abundance could be used as biological indicator for the water quality.