Storms, associated with strong winds and heavy rains, are often the most severe physical disturbances in shallow coastal areas causing instability to sedimentary environments. We hypothesized herein that if storms influence short-term assemblage structure of macrofauna, then assemblages should change after storms, while remaining relatively stable over calm weather conditions. The study was conducted at the subtropical Paranaguá Bay, in southern Brazil. We selected four 700 m² sites, at the estuarine outlet, to monitor changes in number of species, number of individuals and Shannon diversity. Sampling was arranged considering the weather forecast so that both before and after conditions could be recorded. Data of each site was tested separately to access the significance of specific (before/after) comparisons using t tests. There were no clear effects of storms on macrofaunal species richness, abundance and diversity at the four sampled sites. Conversely, we showed that short-term variation in abundances occurred regardless of weather conditions. Increased dispersal may be the most common process associated with storms instead of mortality. Storms that intermittently affect the southern coast of Brazil can be thus seen as minor driving forces of shallow-water estuarine macrofauna. Effects of extreme meteorological events remain to be assessed.