The spatial and temporal variability in the relative abundance of the post-larvae (PL) and juvenile (JU) stages of the pink shrimp Farfantepenaeus paulensis was investigated in the estuary of Lagoa dos Patos, southern Brazil. This analysis enabled the identification of differential distribution patterns. Pink shrimp abundance was studied to understand what factors influence the occupation of the estuary. Monthly samples were taken with a trawl net at 12 sites in the estuary from September 2010 to January 2013. Comparisons were made between protected and unprotected sites. Both PL and JU had a wide distribution in the estuary. The temperature was not a significant variable for explaining abundance variability. The abundance of PL increased with salinity and influenced PL entry to the estuary. The highest abundances of PL were found in unprotected areas and protected sites at the mouth of the estuary, while juveniles were unevenly distributed with higher abundance in protected areas. Recruitment period of PL in the estuary was October to March, and of juveniles was November to February. We suggest that the preservation of unprotected shallow waters and protected areas at the mouth of the estuary are key to further recruitment of the species in the estuary.