The seasonal variability of the benthic community in a shallow sublittoral site was analyzed at the Laguna Estuarine System, a chocked lagoon in South Brazil. Seasonal replicate samples for the microphytobenthos, meiofauna and macrofauna were undertaken from October 2003 to October 2004. The analysis of the different component of the benthos permitted to show a clear temporal asynchrony in the microphytobenthos biomass, meiofauna and macrofauna univariate measures increase and decline. Sediment chlorophyll a and phaeopigments followed a similar seasonal trend, with low biomass in the winter, higher in the summer and intermediate values in spring and autumn. The benthic fauna components of the Laguna Estuarine System also showed a clear seasonal oscillation, but with an opposite pattern of variation. Whilst the number of species and abundance of the macrofauna were significantly higher in the spring and summer, for the meiofauna, both the number of taxa and abundances were significantly higher during the winter and autumn. The results of this study suggested that the divergent seasonal variations of the meiofauna and macrofauna may be linked to their different life strategies, and that biological interactions between meiofauna and macrofauna may also play a significant role in structuring these communites.