Because of decreasing sea-ice extent and increasingly frequent Arctic storms, low-lying coastal ecosystems are at heightened risk from marine storm surges. A major Arctic storm event originating in the Beaufort Sea in September 1999 resulted in the flooding of a large area of the outer alluvial plain of the Mackenzie Delta (Northwest Territories, Canada), and has been previously shown to have caused unprecedented impacts on the terrestrial ecosystems on a regional scale. We use diatoms preserved in lake sediment cores to gain a landscape perspective on the impact of the storm on freshwater systems, and to determine if other such events have occurred in the recent past. Our results indicate that five lakes located at the coastal edge of the low-lying Mackenzie Delta show strong, synchronous, and previously unobserved increases in the relative abundance of brackish-water diatom taxa coincident with the timing of the 1999 storm surge. These changes were not observed at a control site located farther inland. The degree to which the storm surge impacted the chemical and biological limnology of the lakes varied, and was not explained by measured physical variables, suggesting the degree of impact is likely related to a combination of factors including distance from the coast, the size:volume ratio of the lake and its catchment, and water residence time. We show that the 1999 storm surge resulted in unmatched broadscale impacts on the freshwater ecosystems of the outer Mackenzie Delta, and that while minimal recovery may be occurring in some of the systems, the lakes studied remain chemically and biologically impacted more than a decade after the inundation event.