Polychaete abundance and assemblage structure were analysed from 144 zooplankton samples taken in eight seasonal campaigns between October 2007 and November 2008 on Babitonga Bay estuary (south Brazil). A total of 16 taxa were found, classified in three categories: (i) larvae (five taxa) dominated by Loimia sp. (Terebellidae) (up to 59 ind 100 m−3); (ii) syllid epitokes (three taxa) dominated by Procerastea sp.2 (up to 11 ind 100 m−3) and Myrianida sp. (up to 6 ind 100 m−3); and (iii) adults of typically benthic species (eight taxa) which were only occasionally sampled in low densities (<1 ind 100m−3). Larvae dominated mostly during spring and summer in the outer sector of the estuary, while syllid epitokes peaked during winter with higher abundances in the inner sector. The assemblage dynamics match the seasonal and spatial changes in the environmental conditions of the estuary. Descriptive variables explained 49.5% of the polychaetes variance according to Redundancy Analysis. Rainfall, temperature and salinity were the variables most influencing the assemblage, with rainfall and temperature regulating seasonal, and mostly salinity regulating spatial patterns, similar to meroplanktonic populations from both temperate and tropical latitudes. Dominant species had different hydrographic preferences, Loimia sp. was more abundant in warmer (>23°C) and saltier (>25) waters, Magelona papillicornis larvae were more abundant in saltier waters with intermediate temperatures (22–23°C), and the syllids were more common and abundant on lower temperatures (<20°C). In addition we highlight the occurrence of several benthic taxa suspended in the water column, probably due to bottom disturbance.