The blue crab Callinectes sapidus is an important ecological and commercial species. It plays a fundamental role in the structure and function of coastal benthic food webs, with global catches of ~74,357 tons. This is the most exploited portunid species in Brazil. However, few studies about the ecology and population dynamics of C. sapidus have been published. This study aimed to analyse the preferred areas for the spatial distribution of juveniles and moulting individuals of C. sapidus in shallow areas of the Patos Lagoon estuary and the adjacent marine reproductive area, and their relation to water and sediment characteristics. Juveniles and moulting individuals preferred the embayment of the upper estuary, where the sediments are finer, with higher contents of organic matter and the presence of submerged vegetation. There was also a temporal variability in the abundance of juvenile size classes, with two marked increments of smaller individuals: (1) in late spring and summer and (2) in winter, indicating two recruitment peaks. Unusual environmental conditions in the summer of the first year, with an increase of fine sediments and organic matter, combined with low salinities in the adjacent marine area, allowed recruitment of individuals there. We suggest better attention to the embayment around the Marinheiros Island (considered here as upper estuary) for management and protection measures due to the overlapping of recruitment preferences of the blue crab, pink shrimp and fish species in this area.