The vertical zonation of zooplankton in a deep central Baltic Sea basin was studied in relation to hydrography based on vertically resolved sampling. The study period covered different seasonal hydrographic conditions as well as inflow events of water masses from the North Sea, important for the physical condition of this marginal sea. By means of multivariate discriminant function and canonical analysis, we show a distinct vertical zonation of the zooplankton community in the water column. Three main habitats, which reflect the hydrographic situation, were identified with distinct differences in zooplankton composition: (1) the summer surface layer, bound by the thermocline at its lower rim; species inhabiting this layer are only seasonally abundant or forced to adjust to the cooler winter water; (2) the intermediate winter water, bound by the halocline from below and the thermocline or surface as the upper boundary; species dwelling in this layer face a reduced volume and are cut off from the high primary production when their habitat is limited from above by the summer thermocline; (3) the layer between the permanent halocline and the seafloor; the taxonomic composition in this layer shows no significant effect in relation to the observed inflows. The consequences of this zonation for trophodynamic interrelationships and advection processes are discussed. © 2006 Elsevier B.V. All rights reserved.