In contrast to planktonic ecosystems, the fate of bacterial production in aquatic sediments is still largely unclear. In this study, we identified the factors regulating the impact of flagellate grazing on benthic bacterial production for a sandy and a silty intertidal sediment. Flagellate grazing rates were estimated using fluorescently labelled sediment to prevent disturbance of in situ bacterial density and community composition and to account for grazing on attached bacteria. Since flagellate cell size was quite diverse, the grazing rates were determined for 4 size classes. Bacterial production was measured simultaneously with grazing estimates. Bacterial density and production increased with decreasing median grain size of the sediment. Bacterial production was strongly related to the chlorophyll a content of the sediment, indicating resource control of bacterial production. In contrast to bacteria, flagellate biomass decreased with decreasing median grain size of the sediment. Pairwise comparison of grazing rates between the 2 sites showed that grazing rates were significantly higher at the sandy site. This suggests that the effect of sediment composition on flagellate biomass may be mediated by an influence of sediment characteristics on flagellate ingestion rates, The negative relation of bacterial production and the positive relation of flagellate biomass and grazing rates with median grain size resulted in a significant positive relation between the impact of flagellate grazing on bacterial production and the median grain size of the sediment. These results amount to an uncoupling of flagellate grazing and bacterial production in fine sediments. Our results as well as results from previous studies suggest that grazing by flagellates is not an important fate of bacterial production in aquatic sediments, except for sandy sediments during periods of low bacterial production.