Abstract Despite their wide use in past sea-ice reconstructions, the seasonal, habitat and species-based sources of sedimentary sea-ice proxies are poorly understood. Here, we conduct direct observations of the community composition of diatoms, dinoflagellate cysts and highly branched isoprenoid lipids within the sea ice, water column, sediment traps and sediment surface in the Belcher Islands Archipelago, Hudson Bay throughout spring 2019. We find that Arctic diatom and dinoflagellate cysts species commonly used as sea-ice proxies appear to be only indirectly linked to sea-ice conditions, and that the sediment assemblages of these groups overrepresent summertime pelagic blooms. Species contributing to the diverse sea-ice diatom communities are rare in the sediment. Dinoflagellate cysts form a typical Arctic assemblage in the sediment, although they are virtually absent in the sea ice and water column in spring. We also find that certain highly branched isoprenoid lipids that were previously considered indicators of open water, can be produced in sea-ice. We conclude that contextual knowledge and a multiproxy approach are necessary in reconstruction, encouraging further studies on the sources and controls of sea-ice proxy production in different geographic areas.