Calcareous microfossil assemblages in late Holocene sediments from the western Arctic continental shelf provide an important baseline for evaluating the impacts of today’s changing Arctic oceanography. This study compares ¹⁴C-dated late Holocene microfaunal assemblages of sediment cores SWERUS-L2-2-PC1, 2-MC4 and 2-KL1 (57 mwd), which record the last 4200 years in the Herald Canyon (Chukchi Sea shelf), and HLY1302-JPC-32, GGC-30, MC-29 (60 mwd), which record the last 3000 years in the Beaufort Sea shelf off the coast of Canada. Foraminiferal and ostracode assemblages are typical of Arctic continental shelf environments with annual sea-ice cover and show relatively small changes in terms of variability of dominant species. Important microfaunal changes in the Beaufort site include a spike in Spiroplectammina biformis coinciding with a decrease in Cassidulina reniforme in the last few centuries suggesting an increase of Pacific Water influence and decreased sea-ice. There is low-amplitude centennial-scale variability in proportions of benthic foraminiferal species, such as C. reniforme. In addition to these species, Cassidulina teretis s.l., Elphidium excavatum clavatum and Stainforthia feylingi are also common at this site. At the Herald Canyon site in the last few centuries, C. reniforme peaks around 150 years BP and then decreases while Spiroplectammina earlandi spikes and Acanthocythereis dunelmensis decreases also suggesting an increase in Pacific Water influence and decreased sea-ice at this site. This site also includes Buccella spp. and Elphidium excavatum clavatum. Differences in benthic foraminifera and ostracode species dominance between the two sites may be due to a greater influence of Pacific Water in the Chukchi shelf, compared to the more distal Beaufort shelf, which is also affected by the Beaufort Gyre and the Mackenzie River.