Estuarine intertidal flats are important ecosystems characterized by high primary production of microphytobenthos and high secondary production of macro- and meiofauna, especially nematodes. However, the link between both ecosystem components (microphytobenthos and faunal communities) is not fully established yet. In this study, spatial patterns and drivers of nematode density and genus composition were investigated at two different spatial scales (i.e. meso- and microscale), with drivers including sediment granulometry, inundation period and food availability as indicated by various phytopigments. Our study has shown that specific food sources, as represented by different pigments and measures of freshness, are important drivers of nematode genus composition and densities at both scales, especially for the surface layers of the sediments. These food sources mainly comprise microphytobenthos, but also deposited phytodetritus and zooplankton faecal pellets, a resource which had hitherto been largely overlooked in intertidal flats. Tidal level and grain size also had a more pronounced structuring effect in the surface layer of the sediment, while their assumed larger importance at the mesoscale was not outspoken. At both scales, vertical heterogeneity in nematode assemblages was larger than horizontal variability, which has repercussions for future studies into the spatial variability of nematode assemblages of tidal flats.