The effects of cold fronts in a shallow sublittoral system at the Island of Santa Catarina, S Brazil, were investigated in June 2002. Atmospheric, pelagic and benthic data were taken daily covering the days before, during and after the passage of two cold fronts, summing 8 days of sampling. The results clearly showed that the passage of cold fronts, a short-term event, promote changes in the whole shallow sublittoral system, from the pelagic to the benthic one. At the pelagic system, both the cold fronts changed seston, nutrients and chlorophyll a concentrations. The increase in chlorophyll a just after the cold fronts probably resulted from phytoplankton retention and accumulation next to the coast, the microphytobenthos resuspension and the increase in nutrients availability. At the benthic system, sediment features and all of the three benthic components studied- microphytobenthos, meiofauna and macrofauna were also affected by the passage of the cold fronts. The sediments from the studied site suffered a clear homogenizing process. While medium grain size decreased, fine sand percentages gradually increased after the cold front passage. In contrast, sediment organic content was significantly higher just after the first cold front. The effects of the passage of cold fronts in the benthos were dependent on the biological component, the vertical distribution and on the cold front magnitude. The sediment chlorophyll a concentration was lower exactly one day after both cold fronts passage while phaeopigments were significantly higher. The results of the study showed that both macrofauna and meiofauna, particularly nematodes, of the upper layer of the sediment exhibited a decrease in density and number of taxa during the passage of the first frontal system. The nematodes, more than suffering erosion and transport, showed a vertical migration process to the deeper layers of the sediment during the passage of the cold fronts.