We investigated the natural and anthropogenic drivers controlling the spatiotemporal distribution of the meiofauna in the submarine Blanes Canyon, and its adjacent western slope (NW Mediterranean margin of the Iberian Peninsula). We analyzed the relationships between the main sedimentary environmental variables (i.e. grain size, Chl-a, Chl-a: phaeopigments, CPE, organic carbon and total nitrogen) and the density and structure of the meiofaunal assemblages along a bathymetric gradient (from 500 to 2000 m depth) in spring and autumn of 2012 and 2013. Twenty-one and 16 major taxa were identified for respectively the canyon and slope, where the assemblages were always dominated by nematodes. The gradual decreasing meiofaunal densities with increasing depth at the slope showed little variability among stations and corresponded with a uniform pattern of food availability. The canyon was environmentally much more variable and sediments contained greater amounts of food resources (Chl-a and CPE) throughout, leading not only to increased meiofaunal densities compared to the slope, but also different assemblages in terms of composition and structure. This variability in the canyon is only partly explained by seasonal food inputs. The high densities found at 900 m and 1200 m depth coincided with significant increases in food availability compared to shallower and deeper stations in the canyon. Our results suggest that the disruption in expected bathymetric decrease in densities at 900–1200 m water depth coincided with noticeable changes in the environmental variables typical for disturbance and deposition events (e.g., higher sand content and CPE), evoking the hypothesis of an anthropogenic effect at these depths in the canyon. The increased downward particle fluxes at 900–1200 m depth caused by bottom trawling along canyon flanks, as reported in previous studies, support our hypothesis and allude to a substantial anthropogenic factor influencing benthic assemblages at these depths. The possible relationships of the observed patterns and some major natural environmental (e.g., surface productivity or dense shelf water cascading) and anthropogenic (e.g. the lateral advection and downward transport of food-enriched sediments resuspended by the daily canyonflank trawling activities) drivers are discussed.