Estuarine chaetognath population dynamics are poorly known worldwide. We have conducted eight seasonal campaigns (October 2007–August 2008) sampling three sectors in the subtropical Babitonga Bay estuary (26°S 48°W) in order to depict chaetognath abundance and population structure dynamics and test the influence of hydrography and food availability and type. Of three species sampled, Parasagitta friderici represented >93% of abundance in all samples and was examined in detail. There were no differences in P. friderici abundance between the sectors of the estuary, related to its high tolerance to low salinity, a feature not common for most chaetognath species. Salinity tolerance is an important adaptive characteristic to thrive within estuarine systems, and probably is responsible for the dominance of P. friderici in coastal and brackish water environments throughout most of its distribution. Juveniles dominated the population most of the year, except in February–April when abundances were lower and adults predominated. These results suggest that recruitment occurs continuously throughout the year, being more intense between October and January (spring to early summer) and in May (autumn) when densities and proportion of juveniles were higher. General Additive Models suggest that temperature and zooplankton biomass are significant (P < 0.05) factors influencing juvenile abundance while only the latter influenced the adults. We conclude that food availability is the most important driver in the studied population of P. friderici and recruitment peaks, which lead to high densities, seem to occur following peaks of their copepod prey along with particular temperature conditions (22–23°C).