Zooplankton dataset contains data on the species composition, biomass and abundance of meso- and merozooplankton groups. The data are gathered during the Estonian national monitoring of coastal and open seain the Baltic Sea. Samples are collected vertically from three horizons 1) near-bottom to upper halocline layer, 2) halocline top layer to termocline top layer 3) termocline top layer to surface in accordance with the Manual for Marine Monitoring in the COMBINE programme of HELCOM. The samples are analysed using microscopy. Biomass and abundance records are provided for such groups like Rotatoria, Copepoda, Cladocera etc.