Understanding community assembly and processes driving diversity in deep-sea environments is a major challenge in marine ecosystems. In this paper, we investigated the importance of environmental gradients at different spatial scales in structuring deep-sea canyon and continental slope meiobenthic nematode communities in the NW Mediterranean Sea. Three scales were investigated 1) Ecosystem: Blanes Canyon vs. adjacent open slope; 2) Water-depth within each ecosystem: 1500, 1750 and 2000 m; and 3) Vertical profile (three layers within the first 5 cm of sediment). Nematode communities were analysed in terms of density, biomass, diversity and community structure. Grain size, Chl a, Chl a: phaeopigments, CPE, organic carbon and total nitrogen were measured to assess the relationships with nematode assemblages. Blanes Canyon harbours more abundant and diverse assemblages than slope, particularly at 1,750 m and 2,000 m depth respectively. The higher canyon values may be related to the higher food availability observed in the former, which can be a consequence of the so-called “canyon effect”. Slope assemblages were overall more uniform than those in the canyon, where there were greater bathymetrical differences in community structure. Densities in the canyon peaked at 1,750 m depth, which did not correspond with the bathymetric gradient in food availability. The deepest canyon station was the most similar to the slope stations in terms of both environmental conditions and nematode communities, suggesting it lied outside the canyon influence. The higher habitat heterogeneity of the canyon (indicated by its greater vertical sediment profile and water depth differences) played a key role in structuring nematode spatial distribution. Independently of the ecosystem, however, the vertical sediment profile proved to be the most determinative factor for density, community structure, and diversity.