Aquatic ecosystems around the world are threatened by invasions of non-indigenous species (NIS).This study examines the invasion dynamics of a European cladoceran, Eubosmina coregoni, into lakes in Central Canada. Well-preserved cladoceran remains in sediment cores from Lake of the Woods, Ontario, and Lake Winnipeg, Manitoba, provide a historical account of E. coregoni in these water bodies confirming this species is a recent invader. Lead-210 dating of the sediment cores indicates E. coregoni has been present in these water bodies since the late 1980s or early 1990s. Top/bottom sediments from Lake of the Woods show this species is most abundant in the northwest and eastern regions of the lake. Additionally, extant zooplankton samples from Lake Winnipeg reveal that E. coregoni is mostly restricted to the North Basin. Results from this study provide a basis for future investigations of the invasion of E. coregoni and other NIS into these water bodies.