In ultra-oligotrophic lakes and the sea, calanoid copepods are the dominant mesozooplankton and cladocerans are generally sparse or absent. To determine the effects of predation and nutrient enrichment on the pelagic microbial food web of an ultra-oligotrophic lake, we added copepods and cladocerans at low biomasses (<60 mu g l(-1)) to in situ enclosures in Lake Wakatipu, New Zealand, in the presence and absence of added nutrients (nitrogen and phosphorus). In response to nutrient fertilization, the concentrations of phototrophs >3 mu m and heterotrophic bacteria increased by 50 and 15%, respectively, over 4 days, but those of cyanobacterial picoplankton decreased by 68%. The presence of calanoid copepods (Boeckella dilarata) at ambient densities (1 and 4 l(-1)) rapidly and severely suppressed ciliate population growth over 4 days and also lowered that of flagellates >3 mu m, even when microbial growth was enhanced by added nutrients. The presence of a small cladoceran, Ceriodaphnia dubia, at double the densities, but similar biomasses, to those of copepods, depressed the net growth rates of ciliates and flagellates to a lesser degree. The net growth rate of heterotrophic bacteria after 4 days declined with flagellate abundance, consistent with the possibility of regulation by flagellates. Although bacteria and algae increased in response to nutrient fertilization (bottom-up control), predation (top-down control) appeared to play an important role in structuring the microbial food web of this ultra-oligotrophic lake in summer.