Low-lying Arctic coastal environments are threatened by marine storm surges, which are predicted to increase in frequency and intensity as a result of decreasing sea ice, rising sea levels and altered intensity and frequency of storm activity. The Mackenzie Delta of Canada’s Northwest Territories, a vast, low-lying wetland ecosystem, is particularly susceptible to such storm surges, because much of the outer alluvial plain is below 2-m elevation. A large storm-surge event in September 1999 flooded >13,000 ha of alluvial terrain and impacted the terrestrial and freshwater ecosystems of the region. Previous research on the limnological impacts of the storm surge recorded a shift from freshwater to brackish diatom taxa, and a change in cladoceran assemblages to more saline-tolerant species. We examined the remains of Chironomidae (Insecta, Diptera) in sediment cores from two lakes impacted by the 1999 saltwater inundation to determine whether the storm surge also affected benthic macroinvertebrate communities, which are particularly important to lake ecosystem function in Arctic regions. We observed an increase in the relative abundance of saline-tolerant taxa in the two impacted lakes, including Paratanytarsus and Cricotopus/Orthocladius, and decreases in saline-intolerant Sergentia and Corynocera oliveri-type, coincident with the 1999 storm. We observed no major assemblage changes after 1999 in a control lake located beyond the zone of inundation. The number of head capsules recovered from sediments of the impacted lakes increased after the 1999 storm, suggesting no negative impact on overall chironomid abundance as a result of the shift to brackish conditions. There has, however, been no recovery of the chironomid community to the pre-1999 composition. Earlier assemblage changes in both impacted lakes likely tracked regional climate warming in the region, known to have begun in the late nineteenth century.