The increasing impact of human activities, global warming, rising sea levels, and alien species invasion are major drivers of ecological changes in the benthic ecosystems of the Wadden Sea. Repeated benthological and sedimentological investigations have been conducted for intertidal flats, offshore regions, and estuaries. There is a gap in knowledge, however, with respect to the spatial distribution and structure of benthic communities in tidal channel systems of the Wadden Sea. In this study, the spatial distribution of subtidal macrofauna communities in relation to environmental variables in the lesser-known tidal channels of Jade Bay (Wadden Sea of Lower Saxony, southern North Sea) were investigated. In 2009, grab samples were taken at 29 stations, and a total of 98 macrofauna taxa were recorded, with polychaetes predominating. Distinct macrofauna communities among and within the tidal channels were identified using multivariate statistics. Distance-based linear models revealed that tidal current velocity and depth best explained the spatial variation in macrofauna community structure. On a smaller spatial scale, within the tidal channels, the relationships between macrofauna communities and sediment characteristics were greater. Oligochaete species (Tubificoides benedii, Tubificoides pseudogaster, Heterochaeta costata), Peringia ulvae, and polychaetes (Hediste diversicolor, Nephtys hombergii, Streblospio benedicti) showed the highest correlation with the multivariate abiotic data. In addition, species such as the anemone Urticina felina were found to benefit from the presence of hard substrates (patches of gravel), which highlights the importance of local habitat heterogeneity. A comparison among different subtidal basins in the Wadden Sea based on dominant macrofauna species revealed that the macrofauna community structure of Jade Bay showed the greatest similarity with communities of the western Dutch Wadden Sea. In contrast, the greatest dissimilarity was found between the Jade Bay and Sylt communities, likely attributable to differences in sedimentological and hydrodynamical characteristics.