Our knowledge of the functioning of the benthic microbial food web still lags considerably behind that of its pelagic counter part. In addition, there is increasing evidence that the taxonomic composition of the various functional groups within a community may strongly influence the trophic relationships and the carbon flow. We conducted an investigation of the microbial community (bacteria, flagellates, ciliates, meiofauna) of marine, freshwater, and intertidal sediments. Samples were analysed in terms of spatial (between sites) and temporal (samples collected during different seasons in the same site) differences in abundances and community composition. Our study revealed large differences in ciliate species composition. The occurrence of dominant ciliates and their allocation to feeding types indicated that herbivory was the most common and important feeding strategy, while the importance of bacterivory varied significantly among the sediments investigated. Ciliate diversity and species richness, and biomass of ciliates and meiofauna were largely controlled by chlorophyll a concentrations. In contrast, abiotic factors, such as temperature and salinity appeared to have little impact. The ecological implications of our findings will be discussed.