The Labrador Coastal Current (LCC) transports cold and fresh waters of Arctic origin towards the North Atlantic and has a strong influence on the coastal ecosystems and climate of eastern Canada. Here, we present a multi-decadally resolved record of changes in sea-surface and near-bottom conditions of the LCC during the last 3000 years based on the analysis of biogenic tracers (organic-walled dinoflagellate cysts, carbon, and nitrogen geochemistry) and sedimentary content (sortable silt, magnetic susceptibility, elemental ratios) in the upper 2 m of sediments in a core retrieved offshore Nain, Nunatsiavut. Our data reveal multi-centennial bottom flow strength variability in the LCC, with strong linkages to changes in regional ocean circulation patterns. At about 2100- and 550-years BP, the sedimentological and biogenic tracer data suggest changes in the LCC bottom current intensity (decline and strengthening, respectively) that coincide with shifts in the persistent mode of the North Atlantic Oscillation. Our proxy data suggests increased biological production during the last 500 years compared to the preceding 2500 years, possibly reflecting a gradual decrease length of the sea-ice season. The data show a decline in the LCC strength during periods of increased polar water influence identified in previous palaeoceanographic studies conducted further north, which may be attributed to the trapping of freshwater in sea ice during these periods. Our results highlight the dynamical oceanographic and atmospheric factors that influence the LCC and the coastal ecosystems along its path and confirm that the processes in Baffin Bay impact the Labrador Shelf oceanography.