Trophic interactions within the plankton of the lowland River Meuse (Belgium) were measured in spring and summer 2001. Consumption of bacteria by protozoa was measured by monitoring the disappearance of 3H-thymidine-labelled bacteria. Metazooplankton bacterivory was assessed using 0.5-µm fluorescent microparticles (FMPs), and predation of metazooplankton on ciliates was measured using natural ciliate assemblages labelled with FMPs as tracer food. Grazing of metazooplankton on flagellates was determined through in situ incubations with manipulated metazooplankton densities. Protozooplankton bacterivory varied between 6.08 and 53.90 mg C m−3 day−1 (i.e. from 0.12 to 0.86 g C−1 bacteria g C−1 protozoa day−1). Metazooplankton, essentially rotifers, grazing on bacteria was negligible compared with grazing by protozoa (∼1000 times lower). Predation of rotifers on heterotrophic flagellates (HFs) was generally low (on average 1.77 mg C m−3 day−1, i.e. 0.084 g C−1 flagellates g C−1 rotifers day−1), the higher contribution of HF in the diet of rotifers being observed when Keratella cochlearis was the dominant metazooplankter. Predation of rotifers on ciliates was low in spring samples (0.56 mg C m−3 day−1, i.e. 0.014 g C−1 ciliates g C−1 rotifers day−1) in contrast to measurements performed in July (8.72 mg C m−3 day−1, i.e. 0.242 g C−1 ciliates g C−1 rotifers day−1). The proportion of protozoa in the diet of rotifers was low compared with that of phytoplankton (<30% of total carbon ingestion) except when phytoplankton biomass decreased below the incipient limiting level (ILL) of the main metazooplantonic species. In such conditions, protozoa (mainly ciliates) constituted ∼50% of total rotifer diet. These results give evidence that microbial organisms play a significant role within the planktonic food web of a eutrophic lowland river, ciliates providing an alternative food for metazooplankton when phytoplankton becomes scarce.