The macrobenthos is important in benthic remineralization processes; it represents a trophic link and is also often used as a bio-indicator in monitoring programs. Variations of the environmental parameters strongly influence the structure of the macrobenthic communities in the marshes and since macrobenthos is the most important food item for marsh-visiting fish species in the Schelde, the variation in food resources can have a strong effect on the higher trophic level. The present study deals with the variation in macrobenthic communities in different habitats of intertidal marshes along the salinity gradient and the differences between the marsh creeks and the intertidal part of the estuary. The study measured density and species richness together with the biomass, and sampled a large intertidal channel and a smaller creek within five marshes along the salinity gradient of the Schelde estuary every six weeks between May and October in 2000. The small creeks had a smaller grain size and higher organic matter content than those in the large channel although the differences in the environmental parameters did not explain the different communities in the two habitats. Marshes had distinct macrobenthic communities but the abundance of macrofauna fluctuated along the estuary without an identifiable spatial trend. In contrast, the total biomass increased towards the euhaline area due to the domination of Nereis diversicolor. Diversity showed a significant positive correlation with the salinity. Comparison of the macrofaunal communities in the marsh with those on the intertidal flats of the estuary indicated similar trends in density, biomass and diversity along the salinity gradient. The density was similar in both habitats whereas biomass was much higher in the intertidal habitats of the estuary, partly due to the higher biomass of molluscs and annelids. Diversity indices were higher in the marsh, and the freshwater area had more species than in the estuary.