The recent development and refinement of the molecular toolkit to detect ancient DNA in sediment samples (sedaDNA) has allowed the high-resolution reconstruction of ancient ecological communities dating back thousands of years. Specifically, DNA from lake sediment has been used to derive continuous records of ecological community changes through variable paleoenvironmental conditions. These paleoecological reconstructions can be an important tool for understanding how ecosystems may respond to current and future warming, but reliable methods for taxonomic detection are needed in order make optimal use of these bioarchives. In this study, metabarcoding assays targeting vertebrates, bird, and marine fauna have been carried out across a sediment core collected from Lake Qaupat, Baffin Island, Arctic Canada. While Lake Qaupat is currently ~30 m above sea level, it is located below the local marine limit related to isostatic adjustment after deglaciation. Consequently, initial sediment accumulation is in a marine environment. Combined results from the DNA assays indicate a transitional period over which marine-based fauna are systematically replaced by more terrestrial-based fauna. This transition occurs at a predicted age of 7.4 ± 0.2 ka. Ultimately, these data showcase the power of sedaDNA to document dramatic ecosystem changes through a major relative sea level change in the past, with implications for ecological responses to future sea level change.