Coastal lagoons are aquatic environments that are located at the coast-sea interface. Ecologically important, they harbor a high abundance of macroinvertebrates, especially decapod crustaceans. Therefore, the present study investigated the influence of physical factors on the diversity of decapod macrocrustaceans in a Neotropical coastal lagoon and prepared a list of species, with emphasis on new occurrences for this habitat. The study was conducted from January/2013 to January/2014 in a Neotropical coastal lagoon, seasonally connected to the sea. Ecological indices were estimated to understand biotic diversity; in addition, correlations and type II regression were performed on bivariate combinations to assess the degree of interaction between biotic vs. abiotic variables related to lagoon hydrodynamics. Finally, a partial least squares regression was performed to assess such relationships in the multivariate scenario. Field observations revealed a period of interconnection between the lagoon and the sea/estuary in March and complete isolation in October. The most abundant taxa were Penaeus sp., Callinectes sp., C. danae, Pagurus criniticornis and Clibanarius sclopetarius. In the month before total isolation, greater general abundance was recorded, and in the following month, greater diversity, dominance and equitability were recorded. In the multivariate model, only Maximum Wind Gust, Hourly Wind Speed and Minimum Monthly Astronomical Tide were relevant to explain the biotic variations in the lagoon. These results demonstrate that wind and tide can act as proxies for the hydrodynamic analysis of the lagoon in relation to the biotic factors investigated, since they promote seasonal events of opening and isolation of connectivity, contributing to the transport of individuals by carrying water masses. Still, the coastal lagoon presented itself as a place of shelter and foraging for the biota, with emphasis on the genera Penaeus and Callinectes that use the lagoons to complete their life cycle in the sea-estuary transition. This study indicates that coastal lagoons are essential for the life cycle of coastal crustaceans and should be included in management actions to conserve these areas and Neotropical crustacean species.