Continuous and multi-decadal records of faunal abundance and diversity helping to identify the impacts of ongoing global warming on aquatic ecosystems are rare in the coastal Arctic. Here, we used a 50-year-long microfaunal record from a sediment core collected in the Herschel Basin (YC18-HB-GC01; 18 m water depth) to document some aspects of the environmental responses of the southern Canadian coastal Beaufort Sea to climate change. The microfaunal indicators include benthic foraminiferal assemblages, ostracods and tintinnids. The carbonate shells of two foraminiferal species were also analyzed for their stable isotope signatures (δ13C and δ18O). We compiled environmental parameters from 1970 to 2019 for the coastal region, including sea ice data (break-up date, freeze-up date, open season length and mean summer concentration), the wind regime (mean speed, direction of strong winds and the number of storms), hydrological data (freshet date, freshet discharge and mean summer discharge of the Firth and the Mackenzie rivers), and air temperature. Large-scale atmospheric patterns were also taken into consideration. Time-constrained hierarchal clustering analysis of foraminiferal assemblages and environmental parameters revealed a near-synchronous shift around the late 1990s. The microfaunal shift corresponds to an increased abundance of taxa tolerant to variable salinity, turbulent bottom water conditions, and turbid waters towards the present. The same time interval is marked by stronger easterly winds, more frequent storms, reduced sea-ice cover, and a pervasive anticyclonic circulation in the Arctic Ocean (positive Arctic Ocean Oscillation; AOO+). Deeper vertical mixing in the water column in response to intensified winds was fostered by increased open surface waters in summer leading to turbulence, increased particle loading and less saline bottom waters at the study site. Stronger easterly winds probably also resulted in enhanced resuspension events and coastal erosion in addition to a westward spreading of the Mackenzie River plume, altogether contributing to high particulate-matter transport. Increase food availability since ∼2000 was probably linked to enhanced degradation of terrestrial organic carbon, which also implies higher oxygen consumption. The sensitivity of microfaunal communities to environmental variations allowed capturing consequences of climate change on a marine Arctic shelf ecosystem over the last 50 years.