Qikirtajuaq is a long island facing the Inuit village of Akulivik on the northeastern coast of Hudson Bay (Canada) that is rich in archaeological sites. Kangiakallak-1 (JeGn-2), one of the main sites on this island, is a large multicomponent site that includes Dorset and Thule Inuit winter houses. This study documents the dynamics of palaeoenvironmental conditions in the successive occupations of the Kangiakallak-1 settlement based on plant macrofossils, pollen and non-pollen palynomorph analyses and archaeological research. The data indicate that Dorset inhabitants constructed their dwelling at about 772 cal. a BP. The site was reused by the Thule Inuit a few decades later, starting at about 671 cal. a BP. Thus, Kangiakallak-1 is one of the few sites, at least in Nunavik (northern Quebec, Canada), that were rapidly reoccupied by the Thule Inuit after the departure of the Dorset inhabitants, which indicates a possible overlap between the two cultures in the Akulivik region. The palaeoecological data show that both Dorset and Thule inhabitants left clear footprints at the local scale in the form of several nitrophilous species that became established in and near the houses and persisted over a long period. The deposition of domestic waste (including bone fragments, skin, burnt fat and charcoal fragments) inside the subterranean dwellings fertilized the soil and led to the growth of unique nitrophilous plants. These changes transformed the houses into exceptional floristic refuges.