Wet-dry tropical estuaries are extreme environments driven by wet season rainfall and runoff events. The biota associated with these systems are highly adapted to large fluctuations in salinity. There are few examples globally where water extraction for human needs has not yet had a major impact on freshwater flow volumes and seasonal variability in these systems. Therefore, this study examined the importance of seasonally variable flow on intertidal macrobenthic (>0.5 mm mesh size) abundance and species composition in a pristine, wet-dry tropical estuary and nearshore environment. The focus was on intertidal mud-and sandflats where macrobenthos are known to be an important food source for endangered migratory shorebirds and fisheries species in the region. Macrobenthos on the intertidal flats were sampled on four occasions spanning the late-dry, late-flood, and early-dry periods across four years. Across all sites, total macrobenthic abundance was significantly lowest during the late-flood period, when the salinity was low, and highest in the late-dry season, under hypersaline conditions. In the muddy estuarine intertidal flats, the dominant macrobenthic group was polychaetes. In contrast, in the sandy nearshore intertidal flats, bivalves dominated in the late-dry and early-dry. However, during the late-flood, when salinities were at their lowest, the nearshore intertidal flats experienced almost complete loss of bivalves. Although flow had short-term negative effects on some species, it is clear that macrobenthos recruitment back into the intertidal flats had begun once the tide re-established in the early-dry. The differences in the flood response between polychaetes and bivalves likely reflects differences in their life history strategies, with the burrowing and swimming behaviour of polychaetes likely to be providing the ability to seek refuges during low salinity periods. Macrobenthic abundance was also correlated with benthic chlorophyll a concentrations, likely reflecting that both primary and secondary production is impacted by flow. This study suggests that macrobenthos abundance, and species dominance is driven by the seasonal changes in flow in this pristine system, demonstrating the important role of freshwater inputs.