Deep-sea benthic communities and their structural and functional characteristics are regulated by surface water processes. Our study focused on the impact of changes in water depth and food supplies on small-sized metazoan bottom-fauna (meiobenthos) along a bathymetric transect (1200–5500 m) in the western Fram Strait. The samples were collected every summer season from 2005 to 2009 within the scope of the HAUSGARTEN monitoring program. In comparison to other polar regions, the large inflow of organic matter to the sea floor translates into relatively high meiofaunal densities in this region. Densities along the bathymetric gradient range from approximately 2400 ind. 10 cm-2 at 1200 m to approximately 300 ind. 10 cm-2 at 4000 m. Differences in meiofaunal distribution among sediment layers (i.e., vertical profile) were stronger than among stations (i.e., bathymetric gradient). At all the stations meiofaunal densities and number of taxa were the highest in the surface sediment layer (0–1 cm), and these decreased with increasing sediment depth (down to 4–5 cm). However, the shape of the decreasing pattern differed significantly among stations. Meiofaunal densities and taxonomic richness decreased gradually with increasing sediment depth at the shallower stations with higher food availability. At deeper stations, where the availability of organic matter is generally lower, meiofaunal densities decreased sharply to minor proportions at sediment depths already at 2–3 cm. Nematodes were the most abundant organisms (60–98%) in all the sediment layers. The environmental factors best correlated to the vertical patterns of the meiofaunal community were sediment-bound chloroplastic pigments that indicate phytodetrital matter.