Runoff generated from high elevations is the primary source of freshwater for western North America, yet this critical resource is managed on the basis of short instrumental records that capture an insufficient range of climatic conditions. Here we probe the effects of climate change over the past ∼1000 years on river discharge in the upper Mackenzie River system based on paleoenvironmental information from the Peace-Athabasca Delta. The delta landscape responds to hydroclimatic changes with marked variability, while Lake Athabasca level appears to directly monitor overall water availability. The latter fluctuated systematically over the past millennium, with the highest levels occurring in concert with maximum glacier extent during the Little Ice Age, and the lowest during the 11th century, prior to medieval glacier expansion. Recent climate-driven hydrological change appears to be on a trajectory to even lower levels as high-elevation snow and glacier meltwater contributions both continue to decline.