Sediment properties, microphytobenthos biomass (chlorophyll a and phaeopigments), and the structure of the benthic communities of the three main lagoons (Mirim, Imaruí and Santo Antonio) of the Laguna Estuarine System, South Brazil, were analyzed during summer and winter. Microphytobenthos biomass did not differ significantly among the lagoons, but showed higher values in the summer. The macrofauna was characterized by low species richness and the dominance of the gastropod Heleobia australis, the tanaidean Kalliapseudes schubartti and the bivalve Erodona mactroides. The meiofauna was composed of 20 higher taxa and the nematodes dominated in all the lagoons and periods. Desmodora (Desmodora) sp.1, Terschllingia sp. and Microlaimus sp. were numerically the most important among the 74 nematode species registered. This study showed that, in the Laguna Estuarine System, differences in the benthos among lagoons and periods were dependent on the fauna component analyzed. Whilst macrofauna and nematodes were significantly more diverse in the inner stations, in the Mirim Lagoon, the number of meiofauna taxa did not differ significantly among the lagoons and the diversity and evenness were highest in Santo Antonio. These results were a response of the fauna to the salinity oscillations coupled with the heterogeneity of the sediment in the lagoons. The temporal variability of the fauna, macrofauna being more abundant in the summer and meiofauna in the winter, could be related to the different life strategies of these groups.