The most important clines for marine organisms are formed by temperature and salinity. They separate water layers of different conditions and put constraints on the dispersal of zooplankton species. While stenoecious species are bound to a layer euryoecious can even live under non optimal conditions and enter adjacent strata. The spatial overlap of predators with the zooplankton defines the prey-field. Consequently clines may cause inhomogeneous resource distribution in the water column and affect energy transfer within the food web.The hydrography of the central Baltic Sea is characterised by a permanent halocline in approximately 60m depth and a summer thermocline which separates the winter water from the warm surface layer. While the brackish water above the halocline is permanently renewed, the haline waters often face long stagnation before they are replaced during inflow events from the North Sea. To analyse the vertical zooplankton composition in relation to the hydrography of the Bornholm Basin we used a GLOBEC-Germany time series of vertically stacked multinet samples. It covers the period between March 2002 and May 2003 in the Bornholm Basin and includes data from an inflow event.By means of multivariate discriminant function and canonical analysis we show a vertical zonation of the composition in the water column. In this mathematical analysis species contribute with different loadings to distinguish between samples. Three dominant distribution patterns are found:(1) Species inhabiting the warm summer surface layer above the thermocline.(2) Species inhabiting the layer of the winter water, which is temporarily constrained in volume when the thermocline develops.(3) Species inhabiting water masses below the halocline.