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1. The taxonomic composition, abundance and biomass of heterotrophic protists (ciliates, heterotrophic flagellates (HF), rhizopods and actinopods) in the sediment and water column of shallow inlets of the Southern Baltic was studied under a variety of environmental conditions during 1996–1997. A shallow, highly eutrophic station and a deeper, less eutrophic station were compared. 
2. Community biomass ranged from 0.12 to 0.34 μg C cm−3 in the water column and from 1.5 to 105 μg C cm−3 in the sediment. Heterotrophic protists dominated zooplankton biomass at both stations (73% and 84% mean contribution), while they were of minor importance within the zoobenthos. Expressed per unit area, benthic biomass contributed a significant part (44% and 49%) to the total heterotrophic protistan community at both stations. 
3. Although the methodology for counting ciliates and HF was focussed on a high taxonomic resolution, the results reveal some general trends in the distribution of heterotrophic protists: protozooplankton biomass was dominated by flagellates (80% mean biomass contribution) at the shallow station and by ciliates (73% mean biomass contribution) at the deep station. In the benthos at both stations, ciliates were the dominant protozoans, followed by the hitherto little‐studied rhizopods (25% and 35% mean biomass contribution) and flagellates. 
4. The degree of benthic–pelagic coupling differed between taxonomic groups. Benthic and pelagic communities of ciliates showed little taxonomic overlap. In contrast, many heterotrophic flagellate species were found both in the benthos and in the pelagic. These benthic–pelagic species contributed significantly to the biomass of HF in the water column. The planktonic rhizopod community consisted of a subset of those species found in the benthos. 
5. The abundance of benthic and pelagic protists was positively correlated at the shallow station, but taxonomic data indicate that the direct exchange between benthic and pelagic communities was only partly responsible.