The spatial heterogeneity of the nematode community on an intertidal flat (the Molenplaat) in the Westerschelde estuary (SW Netherlands) has been investigated. The extent to which macroscale (km) variability was more important than microscale (m) variability was tested. In addition, the importance of vertical distribution profile in the sediment in explaining the horizontal macroscale variability was evaluated. Differences in the structure of the community were analysed at a kilometre scale at three sites that differed in chemico-physical features. The differences in geochemical and physical conditions on a horizontal scale were reflected in species composition and trophic structure of the nematode communities, and to a much lesser extent in their total abundance and species diversity. Detailed investigation of vertical depth profiles showed more pronounced differences between environmentally divergent sites. Sediment granulometry appears to be important in controlling the fauna in the upper sediment layers. At depth, similar faunal assemblages were found irrespective of sediment granulometry, suggesting that other environmental features are more dominant. Vertically, nematode species showed depth distributions that were indicative of sediment characteristics related to the site-specific hydrodynamic regime. Pronounced vertical segregation of nematode species was observed within sandy sediment under strong hydrodynamic and food-stressed conditions. A surface-dwelling nematode community of large predatory enoplids was separated from a deposit feeding xyalid-microlaimid community in deeper sediment layers (beneath 2 cm). Causal factors for this segregation are thought to be species interactions, feeding strategies and/or physical disturbance. In the finest sediments, with high silt content, almost all nematode species were confined to the upper sediment layers (1.5 cm). A sharp decline in density and diversity with depth was observed. Key factors for this distribution pattern are possibly related to the limited ...