Cercopagis pengoi, a zooplanktivore first discovered in Lake Ontario in 1998, may reduce availability of prey for planktivorous fish. Cercoapgis pengoi is most abundant in late summer and fall. Therefore, we hypothesized that abundance of small zooplankton (bosminids and cyclopoids) species would decrease at that time. To determine if the establishment of C. pengoi was followed by changes in the zooplankton community, seasonal patterns in nearshore zooplankton collected from May to October 1995–2000 were examined. Early summer density of small zooplankton was similar in all years while late summer and fall densities were significantly lower in 1998–2000 than in 1995–1997. The declines of small zooplankton coincided seasonally with the peak in C. pengoi density. Other possible causes for the observed changes in small zooplankton are less likely. High levels of fish predation should have resulted in smaller zooplankton in 1998–2000 than in 1995–1997 and larger declines in Daphnia than other groups. This was not observed. There was no significant decline in chlorophyll-α concentrations or changes in temperature between 1995–1997 and 1998–2000. Therefore, the declines in density of small zooplankton were most likely the result of C. pengoi predation. The effect of C. pengoi establishment on alewives is increased competition for zooplankton prey but C. pengoi has replaced a portion of the zooplankton biomass and adult alewife diet formerly dominated by Diacyclops thomasi and Bosmina longirostris.