A 2,000 year-long oceanographic history, in sub-centennial resolution, from a Canadian Beaufort Sea continental shelf site (60meters water depth) near the Mackenzie River outlet is reconstructed from ostracode and foraminifera faunal assemblages, shell stable isotopes (delta 18O, delta 13C) and sediment biogenic silica. The chronology of three sediment cores making up the composite section was established using 137Cs and 210Pb dating for the most recent 150 years and combined with linear interpolation of radiocarbon dates from bivalve shells and foraminifera tests.Continuous centimeter-sampling of the multicore and high-resolution sampling of a gravity and piston core yielded a time-averaged faunal record of every approximately 40 years from 0 to 1850 CE and every approximately 24 years from 1850 to 2013 CE. Proxy records were consistent with temperature oscillations and related changes in organic carbon cycling associated with the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA). Abundance changes in dominant microfossil species, such as the ostracode Paracyprideis pseudopunctillata and agglutinated foraminifers Spiroplectammina biformis and S. earlandi, are used as indicators of less saline, and possibly corrosive/turbid bottom conditions associated with the MCA (approximately 800 to 1200 CE) and the most recent approximately 60 years (1950–2013). During these periods, pronounced fluctuations in these species suggest that prolonged seasonal sea-ice melting, changes in riverine inputs and sediment dynamics affected the benthic environment. Taxa analyzed for stable oxygen isotope composition of carbonates show the lowest delta 18O values during intervals within the MCA and the highest during the late LIA, which is consistent with a 1 degree to 2 degree C cooling of bottom waters. Faunal and isotopic changes during the cooler LIA (1300 to 1850 CE) are most apparent at approximately 1500 to 1850 CE and are particularly pronounced during 1850 to approximately 1900 CE, with an approximate 0.5 per mil increase in delta 18O values of carbonates from median values in the analyzed taxa. This very cold 50-year period suggests that enhanced summer sea ice suppressed productivity,which is indicated by low sediment biogenic silica values and lower delta 13C values in analyzed species. From 1900CE to present, declines in calcareous faunal assemblages and changes in dominant species (Cassidulina reniforme and P. pseudopunctillata) are associated with less hospitable bottom waters, indicated by a peak in agglutinated foraminifera from 1950 to 1990 CE.