We document the rapid transformation of one of the Earth's last remaining Arctic refugia, a change that is being driven by global warming. In stark contrast to the amplified warming observed throughout much of the Arctic, the Hudson Bay Lowlands (HBL) of subarctic Canada has maintained cool temperatures, largely due to the counteracting effects of persistent sea ice. However, since the mid-1990s, climate of the HBL has passed a tipping point, the pace and magnitude of which is exceptional even by Arctic standards, exceeding the range of regional long-term variability. Using high-resolution, palaeolimnological records of algal remains in dated lake sediment cores, we report that, within this short period of intense warming, striking biological changes have occurred in the region's freshwater ecosystems. The delayed and intense warming in this remote region provides a natural observatory for testing ecosystem resilience under a rapidly changing climate, in the absence of direct anthropogenic influences. The environmental repercussions of this climate change are of global significance, influencing the huge store of carbon in the region's extensive peatlands, the world's southern-most polar bear population that depends upon Hudson Bay sea ice and permafrost for survival, and native communities who rely on this landscape for sustenance. © 2013 The Author(s) Published by the Royal Society. All rights reserved.