Great Slave and Great Bear Lakes, the two largest lakes in northern Canada, are similar with respect to their high latitude locations, regional climates, large surface areas and water volumes. They are dissimilar hydrologically. Great Slave Lake is part of the flow-through system of the Mackenzie Basin, whereas Great Bear Lake is hydrologically isolated with all of its inflow and outflow derived from its immediate watershed. Great Slave Lake’s outflow into the Mackenzie River is more than eight times that from Great Bear Lake. Input from the south primarily via the Slave River provides 82% of this outflow volume. These hydrological differences exert pronounced effects on the thermodynamics, hydrodynamics and surface climates of each lake. Although, both lakes have regional annual air temperatures within 2^oC of one another, Great Slave Lake exhibits a much longer open water period and higher water temperatures than Great Bear Lake. During the period when the lakes are warming, each lake exerts a substantial over-lake atmospheric cooling and in the period when the lakes are cooling, each exerts a strong over-lake warming. This local cooling and warming is greatest over Great Bear Lake. Temperature and humidity inversions are frequent early in the lake-warming season and very strong lapse gradients occur late into the lake-cooling season. Annually, for both lakes, early ice break-up is matched with late freeze-up. Conversely, late break-up is matched with early freeze-up. The magnitudes of mid-lake latent heat fluxes (evaporation) and sensible heat fluxes from Great Slave Lake are substantially larger than from Great Bear Lake during their respective open water periods. Most of these differences are attributed to the very different hydrological regimes of the two lakes.