A considerable portion of the pelagic energy flow in the Visvijver Lake, a shallow eutrophic lake, and the Schelde estuary, a eutrophic freshwater tidal zone is channeled through a highly dynamic heterotrophic food web. Microbial food web is using size fractionation method to truncate the grazer chain at predetermined size over 3 or 4 days interval, three experiments revealed the trophic interactions within the microbial food web and the predation effects on the microbial food web from the dominant species of metazooplankton in these freshwater ecosystems. From the predator-prey relationships, trophic cascades were observed. Size fractionation method was evaluated to be efficient for isolating the functional groups (bacteria, HNF, ciliates, rotifers, copepods or Daphnia) in the pelagic food web. In the Visvijver Lake and the Schelde estuary, some structures in the microbial food web were found: bacteria were grazed by HNF as well as ciliates and in turn HNF was grazed by ciliates. But the influence of the different dominant metazooplankton in the experiment was quite different. Daphnia produced significant grazing pressure on bacteria and HNF but not ciliates; copepods and rotifers did not display feeding effects on the components of the microbial food web. Copepod nauplii belonging to 30-200 µm size fraction showed significant predation on ciliates. The contradictive feeding behaviors from our experiment suggest that only investigation on the functional groups in planktonic food web is not enough due to the complexity and variability of predation-prey mechanism among different species even in one group. Only one trophic cascade existed in the experiments: the growth of HNF increased since copepod nauplii captured ciliates, the predator of HNF. The omnivory of ciliates and Daphnia maybe play a role to reduce the influence of trophic cascades.