Meroplankton was investigated at 11 Stations in the southern Kara Sea and the Yenisei Estuary in August 2000. Larvae of 31 benthic taxa representing 10 higher groups were identified. Meroplankton was present almost at all stations and depth levels. The two most abundant groups were Echinodermata (68%) and Polychaeta (26%). Echinoderms dominated total meroplankton locally due to mass occurrences of Ophiopluteus larvae. The relative group composition was highly variable and seemed to depend mainly on the local hydrographic pattern. Comparison of meroplanktonic data with the distribution of the adults revealed for Spionida and Bivalvia a downstream transport of the larvae while for other polychaete species and Ophiuroida upstream transport into the estuary occured. The transport mechanisms and concentration of the larvae within the estuary is explained by physical barriers established by hydrographic gradients, the prevailing mixing processes and the presence of near-bottom counter current.