The western Antarctic Peninsula is experiencing dramatic climate change as warm, wet conditions expand poleward and interact with local physics and topography, causing differential regional effects on the marine ecosystem. At local scales, deep troughs (or canyons) bisect the continental shelf and act as conduits for warm Upper Circumpolar Deep Water, with reduced seasonal sea ice coverage, and provide a reservoir of macro- and micronutrients. Shoreward of many canyon heads are Adélie penguin breeding colonies; it is hypothesized that these locations reflect improved or more predictable access to higher biological productivity overlying the canyons. To synoptically assess the potential impacts of regional bathymetry on the marine ecosystem, 4 major canyons were identified along a latitudinal gradient west of the Antarctic Peninsula using a high-resolution bathymetric database. Biological-physical dynamics above and adjacent to canyons were compared using in situ pigments and satellite-derived sea surface temperature, sea ice and ocean color variables, including chlorophyll a (chl a) and fucoxanthin derived semi-empirically from remote sensing reflectance. Canyons exhibited higher sea surface temperature and reduced sea ice coverage relative to adjacent shelf areas. In situ and satellite-derived pigment patterns indicated increased total phytoplankton and diatom biomass over the canyons (by up to 22 and 35%, respectively), as well as increases in diatom relative abundance (fucoxanthin:chl a). While regional heterogeneity is apparent, canyons appear to support a phytoplankton community that is conducive to both grazing by krill and enhanced vertical export, although it cannot compensate for decreased biomass and diatom relative abundance during low sea ice conditions.