Primary production and organic material sinking export were investigated in the Hudson Bay system (i.e., Hudson Bay, Hudson Strait and Foxe Basin) under ice-free conditions during early fall 2005, using the 14C-uptake method and short-term free-drifting particle interceptor traps deployed below the euphotic zone at 50 m. Principal component analysis revealed spatial patterns of primary production and chlorophyll a (chl a) biomass in the euphotic zone that were shaped by hydrographic conditions and nutrient concentrations linked to freshwater/seawater influence. Primary production rates varied widely, from 70 to 435 mg C m–2 d–1 , while the range of particulate organic carbon (POC) sinking fluxes was narrow, from 50 to 77 mg C m–2 d–1 . Consequently, high ratios of POC sinking export to primary production (i.e., export ratios; range of 0.38–0.69) were observed at stations where primary production was low and dominated by small cells, and where heterotrophic protist dominated in biomass. These results show that at short temporal scales neither protist community structure nor biomass or production rates could be used to predict the magnitude of POC sinking export from the euphotic zone.