Here we present the fossil dinocyst assemblages established from three sediment cores collected along an inshore–offshore transect in the Mackenzie Trough during the 2004 CASES (Canadian Arctic Shelf Exchange Study) cruise. The chronology of each core was determined using 210Pb activity and AMS-14C measurements in core 912A. Sediment cores 912A, 909B and 906B cover the last 600, 200 and 100 years respectively. Palynomorph influxes increase from the bottom to the top of each core, illustrating an increasing productivity over the last 600 years until 1850 AD, when we observe a decrease of productivity until today. We determined a succession of two assemblages over the last 600 years. Assemblage I, at the base of each core, is mostly composed of dinocysts from heterotrophic taxa. The modern assemblage (Assemblage II at the top of each core) is mostly composed of dinocysts from autotrophic taxa. Quantitative reconstructions of sea-surface parameters reveal a sharp increase in summer (August) temperature ( 2 to 5 °C) throughout the study area from 1400 AD until 1800–1850 AD, after which the increase (between 0.5 and 1.0 °C) is much slower until modern times.