Marine cold-spells are an understudied phenomena which can both negatively impact marine wildlife and provide thermal refugia for species displaced by climate change. To develop forward-looking and climate-ready management schemes, it is critical to examine how marine species respond to cold-spells, how long-term warming will affect marine cold-spells over the next century, and how these future cold-spells will in turn affect species of conservation concern, particularly in marine protected areas. To this end, we detect marine cold-spells across the California Current System, a productive Eastern Boundary Upwelling System, relative to a fixed baseline (1980–2009) and to a detrended time series that isolates cold-spells from long-term climate change. We then project the impact of future marine cold-spells on habitat suitability for two endangered top predators: leatherback turtles ( Dermochelys coriacea ) and blue whales ( Balaenoptera musculus ). Models project that 68–99% of the California Current System will no longer experience fixed baseline marine cold-spells by 2099 under a high emissions scenario, though marine cold-spells will still occur relative to a detrended time series. Blue whales lost 5% of their core habitat in National Marine Sanctuaries during historical marine cold-spells and are projected to gain 1–2% more core habitat during future, fixed baseline marine cold-spells. Leatherback sea turtles had little core habitat change during historical marine cold-spells but are projected to gain 4–5% more core habitat during future marine cold-spells. It is plausible that both species gain habitat during future marine cold-spells because these events provide thermal refugia to their prey. We urge conservationists and ecologists to increase their attention to marine cold-spells as potential thermal refugia and prioritize collecting data on endangered species’ prey in order to understand more deeply how species will respond to extreme temperature events.