The Laurentian Great Lakes is an ecosystem that has been vulnerable to non-native species introduction and invasion from sources across the globe. Detecting and responding to non-native zooplankton species presents unique challenges for researchers and managers. Many of these organisms are microscopic and identifying them often requires extensive monitoring and taxonomic expertise. After the initial detection tasks include estimating their source and evaluating potential impacts on native zooplankton and other organisms. Zooplankton have an intermediate trophic status and thus introductions could potentially affect grazing of phytoplankton as well as the forage base for fish. Most recognized are the past invasions of predatory cladocerans (Bythotrephes longimanus Leydig 1860 and Cercopagis pengoi Ostroumov 1891) that have expanded to all five Great Lakes and caused significant damage to the ecosystem and economy (Yan et al. 2011). This thesis provides more recent examples of nonnative zooplankton species detection. Chapter 1 highlights the importance of exploratory monitoring of high traffic harbor areas with our discovery of Diaphanosoma fluviatile Hansen 1899 in the Maumee River in Toledo, Ohio. After this initial detection, further sampling using open lake long term monitoring programs revealed that D. fluviatile had expanded throughout Lake Erie’s western basin. Chapter 2 provides a second case study exploring epibenthic habitats in large lakes rich in cladocerans but poorly monitored. We surveyed the epibenthic region of Lake Ontario using benthic grabs and supplemented this survey with genetic analysis of the cytochrome oxidase 1 gene (CO1). Lake Ontario’s epibenthos included 16 different cladoceran species that were found as deep as 63 meters. Both case studies summarize improved efforts to assess biodiversity in the Great Lakes and to improve the detection of new nonnative zooplankton species introductions.