Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remains unknown. Here, we integrate paleogenomics and stable d13C and d15N isotope analysis to investigate 700 years of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which based on radiocarbon dating span three time periods (1290-1440 CE 1450-1650 CE 1800-1870 CE), indicate shifts across time in the sex ratio of the harvested belugas. An equal number of females and males were harvested in 1450-1650 CE versus more males harvested in the other time periods may reflect changes in hunting practices or temporal shifts in the availability of belugas. We find shifts and sex-based differences in d13C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered novel mitochondrial diversity in the Mackenzie Delta belugas, but we found no changes in genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 years surveyed, indicating the impact of the Inuvialuit subsistence harvest on the genetic diversity of contemporary beluga individuals has been negligible.