We present continuous bi-weekly to bi-monthly dinoflagellate cyst, tintinnid loricae and tintinnid cyst fluxes at two mooring sites in Hudson Bay (subarctic Canada) from October 2005 to September 2006. The total dinoflagellate cyst fluxes at the site on the western side of the bay ranged from 4600 to 53,600 cysts m− 2 day− 1 (average 20,000 cysts m− 2 day− 1), while on average three times higher fluxes (average 62,300 cysts m− 2 day− 1) were recorded at the site on the eastern side of the bay with a range from 2700 to 394,800 cysts m− 2 day− 1. These values are equivalent to the average fluxes calculated from the top 1-cm sediment layer of 210Pb-dated box cores at corresponding locations, and hence lend support to the use of sediment dinoflagellate cysts in palaeoceanography. Tintinnid fluxes ranged from 1200 to 80,000 specimens m− 2 day− 1 (average 32,100 tintinnids m− 2 day− 1) in the west, and 1600 to 1,240,800 specimens m− 2 day− 1 (average 106,800 tintinnids m− 2 day− 1) in the east, with the highest Salpingella sp. fluxes recorded during the sea-ice cover season.