The data set contains palynological data and sea-surface reconstruction data from 65 samples in a sedimentary sequence of the eastern Hudson Bay that covers the last 3000 years. The data are presented vs depth and calibrated ages BP. The palynological data set includes time series of the concentrations of the main palynomorph types, the percentage of taxa in dinocyst assemblages, the percentage of pollen and spore types in the pollen assemblages. The sea-surface estimates from the dinocyst data using the modern analogue techniques include time series of sea-surface temperature and salinity in summer, seasonal extent of sea-ice cover and primary productivity.