Within the framework of the DosMares project, we investigated the standing stocks, structural and functional diversity and community structure of the nematode assemblages both along a bathymetric gradient, and the vertical sediment profile (0–5 cm) in the Blanes Canyon (NW Mediterranean) during autumn 2012. The standing stocks (total density and biomass) did not follow the traditional pattern of bathymetric decline, showing disrupting peaks at 1200 and 1750 m depth. Along the sediment profile, high densities occurred in surface sediment layers, mainly due to increased nematode abundance, while biomass did not show clear general trends. Structural and functional diversity did not exhibit consistent bathymetric gradients, and were not related to sedimentary variables, except for positive correlations with clay and silt contents. However, structural and functional diversity decreased significantly along the vertical sediment profile. The analysis of the nematode community assemblages allowed us to identify three different community structure zones along the canyon axis: upper (ca. 500–1200 m depth), middle (ca. 1500–1750 m depth) and deeper (ca. 2000 m depth), which were 1) followed the canyon topographic heterogeneity, 2) supported by the environmental analyses (food sources and grain size), and 3) were reflected in the variable sediment and organic matter inputs from canyon walls and adjacent margins. The nematode distribution along the vertical sediment profile also varied in the three zones, mainly owing to differences in the respective surface sediment layers. Deeper sediment layers were similar, mainly caused by to the high abundance of Sabatieria. Our results indicate that, in addition to the expected influence of the canyon’s topography and hydrodynamic regimes, the nematode community from Blanes Canyon were controlled by the sedimentary characteristics and available food sources. Moreover, our results and additional data from other research in and around Blanes Canyon suggest that observed anthropogenic pressure in the surrounding areas (mainly derived from regular and persistent trawling activities) plays a key role in explaining the sedimentary pattern along the canyon axis and the observed nematode assemblage distribution.