Climate change will alter marine species composition and abundance with consequences for food webs and ecosystem services. This study used an ensemble modeling approach to project changes in marine ecosystems in Canada’s Exclusive Economic Zone under four climate change scenarios. The business-as-usual scenario resulted in substantial declines in animal biomass in the Pacific and Atlantic EEZ yet increases in the Arctic. Lower emissions resulted in smaller changes highlighting the benefits of stronger mitigation targets. These different future trajectories will require region-specific conservation and management strategies.