We combined sediment and faunal data to explore the role of the sedimentary regime in shaping the distribution of subtidal sandbank environments and the associated meiofaunal nematode communities at Broken Bank and Swarte Bank, in the southern North Sea. A variety of sediment transport processes occur in the area, differing in the frequency and magnitude of sediment mobility, and the continuum between erosion, translation and sediment accumulation. The seabed contained a variety of bedforms, including longitudinal furrows, and small to very large sandwaves. The bed sediments were dominated by fine and medium sands, with admixtures of silt and gravel. Based on sedimentary bedforms and grain size analysis, a total of 11 sedimentary facies were delineated, of which 8 were analysed in detail for their relationships with the meiofauna. The sedimentary facies fell clearly into groups of facies, respectively representing high, high-moderate and moderate, and episodic sediment mobility. For those sedimentary facies where daily movement of sediments and bedforms occurred (‘high’ sediment mobility), the resulting spatially homogeneous environments were dominated by an impoverished nematode community comprising small deposit feeders and large predators. Resistance to sediment movement and the ability to exploit alternative food sources were prominent functional features of the successful colonisers. Those facies characterised by relatively infrequent sediment mobility (‘episodic’ and ‘high-moderate and moderate’ sediment mobility) comprised a heterogeneous suite of benthic habitats, containing taxonomically and functionally diverse assemblages of nematodes of various sizes, feeding types and reproductive potential. Faunal distribution patterns here indicated trade-offs between the resistance to sediment movement, environmental tolerance and competitive abilities. Our focus on diverse assemblages of organisms with high turnover times, inhabiting highly dynamic sedimentary environments, has revealed new animal-sediment relationships of relevance to pure and applied science.