The spread of nonindigenous species (NIS) over land and via interconnecting water bodies is threatening aquatic ecosystems worldwide. This study examines the invasion of the first known NIS zooplankter, Eubosmina coregoni, into Lake Winnipeg, Manitoba, Canada. Analyses of cladoceran microfossils from a sediment core collected in the North Basin of the lake indicate this species first appeared in sediments dated to the late 1980s. An increase in total cladoceran accumulation rates coupled with increasing N, C, P, and chlorophyll a over the last 40 years provides evidence of eutrophication. Extant samples from fall 2002–2005 indicate that E. coregoni is mainly restricted to the North Basin while Bosmina longirostris is present throughout the lake. Results from this study provide baseline data regarding the invasion and establishment of E. coregoni, a precursor to future NIS that may have substantial ecological and economic impacts on the Lake Winnipeg ecosystem.