Recent changes in climate and eutrophication have caused increases in oxygen depletion in both freshwater and marine ecosystems. However, the impact of oxygen stress on zooplankton, which is the major trophic link between primary producers and fish, remains largely unknown in lakes. Therefore, we studied 41 lakes with different trophic and oxygen conditions to assess the role of oxygen stress on zooplankton communities and carbon transfer between phytoplankton and zooplankton. Samples were collected from each lake at the peak of summer stratification from three depth layers (the epilimnion, metalimnion, and hypolimnion). Our results revealed that freshwater zooplankton were relatively tolerant to anoxic conditions and the greatest changes in community structure were found in lakes with the highest oxygen deficits. This caused a switch in dominance from large to small species and reduced the zooplankton biomass in lower, anoxic layers of water, but not in the upper layers of water where the oxygen deficits began. This upper anoxic layer could thus be a very important refuge for zooplankton to avoid predation during the day. However, the reduction of zooplankton in the lower water layers was the main factor that reduced the effectiveness of carbon transfer between the phytoplankton and zooplankton.