The macrozooplankton and micronekton community of the Lazarev Sea (Southern Ocean) was investigated at 3 depth layers during austral summer, autumn and winter: (1) the surface layer (0–2 m); (2) the epipelagic layer (0–200 m); and (3) the deep layer (0–3000 m). Altogether, 132 species were identified. Species composition changed with depth from a euphausiid-dominated community in the surface layer, via a siphonophore-dominated community in the epipelagic layer, to a chaetognath-dominated community in the deep layer. The surface layer community predominantly changed along gradients of surface water temperature and sea ice parameters, whereas the epipelagic community mainly changed along hydrographical gradients. Although representing only 1% of the depth range of the epipelagic layer, mean per-area macrofauna densities in the surface layer ranged at 8% of corresponding epipelagic densities in summer, 6% in autumn, and 24% in winter. Seasonal shifts of these proportional densities in abundant species indicated different strategies in the use of the surface layer, including both hibernal downward and hibernal upward shift in the vertical distribution, as well as year-round surface layer use by Antarctic krill. These findings imply that the surface layer, especially when it is ice-covered, is an important functional node of the pelagic ecosystem that has been underestimated by conventional depth-integrated sampling in the past. The exposure of this key habitat to climate-driven forces most likely adds to the known susceptibility of Antarctic pelagic ecosystems to temperature rise and changing sea ice conditions.