Estuaries are coastal water bodies with great economic and biological importance. The benthic organisms play a significant role in these environments as regulators or modifiers of physical, chemical and biological processes. This study aimed to evaluate the spatial and temporal distribution of the infralittoral decapods in the Itajaí-Açu estuary, investigating factors that influence their distribution and possible effects of a flood event on the benthic community. Six sampling points were established along the longitudinal gradient of the estuary. Monthly samples were taken with otter trawls between May 2008 and July 2010. Crustaceans were separated, packed in labeled plastic bags and kept frozen until processing. Physicochemical data of the water column were also collected with the aid of a multianalyser. In the laboratory the organisms were identified, measured and weighed individually. The analysis of variations in relative abundance and biomass of the species and the analysis of the environmental variables were conducted by using descriptive statistics. The relationship of environmental variables with the biotic variables was examined by Spearman correlation coefficient (p < 0.05). Box-plot graphics of environmental variables in which the main species occurred were generated to identify ranges of environmental conditions under which each species occurred. The results showed that pH, salinity and dissolved oxygen are related to the penetration of the salt wedge, while temperature shows a seasonal pattern. The estuary showed a low richness (14 species), mainly in the two months after the flood of November 2008, and high dominance. It was possible to realize that many factors act on the estuary which make difficult to establish relationships between the biota and environmental variables in particular. There was an increase in abundance and biomass between February and July 2009, which suggest that the fauna was able to recover from the flood.