Most deep-sea organisms feed on the organic matter produced in surface waters and settle on the seafloor. In polar regions, sea ice algal detritus and phytoplankton detritus are the main food sources for benthic fauna that reach the seafloor in pulses. Climate change affects the extension and duration of sea ice cover, which may affect the quantity and quality of food reaching the seafloor, resulting in less ice algae and more phytoplankton biomass. We conducted onboard pulse-chase experiments using sediment cores collected from Baffin Bay, Amundsen Gulf, and the Beaufort Sea to study how macroinfaunal communities in the Canadian Arctic use both food sources. Dual-labeled (13C and 15N) diatoms, Thalassiosira nordenskioeldii (phytoplankton treatment) and Synedra hyperborea (ice algae treatment), were used as tracers of food consumption by macroinfaunal groups. Community structure was analyzed in each region and differences were found among sites. The total uptake of both food sources was higher in Baffin Bay; the macroinfaunal biomass was the highest, with facultative filter/surface-deposit feeders accounting for more than 70% of the total biomass. The Baffin Bay station was the only location where there were notable variations in the biomass-specific uptake of ice algae and phytoplankton detritus by the bivalves and polychaetes, as well as by the community as a whole. At the same time, both food sources were consumed in equal quantities at the Amundsen Gulf and Beaufort Sea stations. This suggests that ice algae are not preferentially uptaken, and macroinfaunal communities may be resilient to a decrease in ice algal input to the seafloor inflicted by sea ice reduction.