Metazooplankton are potentially important links between classical food chains and pelagic microbial food-webs of lakes. We determined the short-term effects of nutrient enrichment and predation on the microbial food-webs of oligotrophic Lake Manapouri and eutrophic Lake Hayes, New Zealand, in summer, by adding calanoid copepods (Boeckella hamata Brehm) and cladocerans (Daphnia carinata King) to in situ enclosures in the presence and absence of added nutrients (nitrogen, phosphorus). In Lake Manapouri, bacteria and phytoplankton, but not picocyanobacteria, increased in response to nutrients; Daphnia reduced the densities of phytoplankton, bacteria, heterotrophic nanoflagellates (HNF), and ciliates; and Boeckella lower the densities of HNF and ciliates. In Lake Hayes, the growth of bacteria, HNF, and phytoplankton, including eukaryotic picoautotrophs, was enhanced by enrichment; Daphnia depressed the concentrations of picoautotrophs and HNF, whereas Boeckella decreased the density of ciliates. In both lakes, Boeckella removed ciliates at higher rates per unit biomass than Daphnia. Our study provides clear evidence of stimulation and inhibition of picoplankton by nutrients, and of potential consumer-mediated control of microbial food-webs by crustacean zooplankton.