The fish-hook flea, Cercopagis pengoi, is an abundant invasive zooplankton that invaded six of the eleven New York Finger Lakes in 1999, one year after invading Lake Ontario. Cercopagis is predatory, which could alter trophic dynamics of invaded lakes since their food webs are dominated by herbivorous zooplankton. Additionally, Cercopagis is consumed by the region’s planktivorous fish (Alosa pseudoharengus), and may impact their trophic position if they shift from consuming the native herbivorous zooplankton to a diet including the invasive predatory zooplankton. The partial New York Finger Lakes invasion creates a natural experiment ideal for studying the impacts of Cercopagis in invaded lakes and the factors preventing establishment in the non-invaded lakes. This study compares ecosystem characteristics of invaded and non-invaded lakes, including physical parameters, productivity, zooplankton assemblages, and alewife characteristics. High predation from alewife likely prevents the establishment of Cercopagis in non-invaded lakes; these lakes have many characteristics indicative of high alewife densities including poorer alewife condition, and a larger proportion of small bodied to large bodied zooplankton. Other differences include invaded lakes containing significantly more predatory zooplankton and fewer Bosmina, a small herbivorous zooplankton that is likely a key prey item for Cercopagis. Despite the presence of more predatory invertebrates, analysis of alewife gut contents indicated that alewife from invaded and non-invaded lakes are likely feeding at a similar trophic position.