This one-year study investigated spatial and temporal variations in the abundance and biomass of the pink shrimp species, Farfantepenaeus paulensis and Farfantepenaeus brasiliensis, in the Conceição Lagoon, southern Brazil (September 2003–August 2004). The influence of salinity, water temperature, and rainfall on shrimp distribution was evaluated. Shrimps were caught monthly at three areas within the Conceição Lagoon (Canto, CA; Centro, CE; and Costa, CO). A total of 744 shrimps were sampled, with F. brasiliensis being the dominant species. The two penaeid species were present throughout the year and significant differences were observed between seasons, with F. paulensis being more abundant during the summer and F. brasiliensis in the autumn, suggesting differential migration timing to the sea, differences in recruitment time and an ontogenetic temporal partitioning. Farfantepenaeus paulensis exhibited a homogeneous spatial distribution, whereas F. brasiliensis was more abundant in CE and CO, suggesting that habitats in this coastal lagoon are heterogeneous. Among the abiotic factors, temperature and salinity seemed to be important variables in defining seasonal and spatial patterns, respectively, of the abundance of F. brasiliensis.