An increase in the frequency and intensity of marine storm surges is a predicted consequence of climate warming, and therefore it is important to better understand the biological responses to such events in coastal regions. In late September 1999, a major storm surge resulted in a saltwater intrusion event over a large area of the Mackenzie Delta (NT, Canada) front, causing rapid salinization of lakes on the alluvial plain. Due to a lack of long-term ecological monitoring data in the region, the impacts that the saltwater intrusion event had on the biota of affected lakes were unknown. We used high-resolution paleolimnological approaches to reconstruct past assemblage changes in Cladocera from impacted Lake DZO-29 (unofficial name) in order to determine how different cladoceran species responded to a major increase in lake salinity following the 1999 storm surge. Camptocercus were extirpated from the lake following the saltwater intrusion and have not recovered. We also observed an initial decrease in Alona relative abundance following the marine flooding, likely reflecting a loss of A. quadrangularis, A. barbulata, and A. costata from the lake. A. circumfimbriata, Chydorus biovatus, C. brevilabris, and Bosmina spp. were abundant both before and after the saltwater intrusion, and Paralona pigra was present following the storm surge, but not prior to it. The most notable shift in Cladocera in the recent sedimentary record, however, occurred much earlier, with an increase in pelagic Bosmina taxa and a subsequent decrease in the benthic/littoral taxa Chydorus and Camptocercus, an assemblage shift that is consistent with a response to climate warming in this region, and strongly correlated to other changes in the lake inferred to be as a result of regional warming.