Great Slave Lake and Great Bear Lake have large surface areas, water volumes, and high latitudinal positions; are cold and deep; and are subject to short daylight periods in winter and long ones in summer. They are dissimilar hydrologically. Great Slave Lake is part of the Mackenzie Basin flowthrough system. Great Bear Lake is hydrologically isolated in its own relatively small drainage basin and all of its inflow and outflow derive from its immediate watershed. Great Slave Lake’s outflow into the Mackenzie River is more than 8 times that from Great Bear Lake. Input from the south 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. The quantitative results in this study are based on limited datasets from different years that are normalized to allow comparison between the two lakes. They indicate that both lakes have regional annual air temperatures within 2°C of one another, but Great Slave Lake exhibits a much longer open-water period with higher temperatures than Great Bear Lake. During the period when the lakes are warming, each lake exerts a substantial overlake atmospheric cooling, and in the period when the lakes are cooling, each exerts a strong overlake warming. This local cooling and warming cycle 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 in the lake-cooling season. Annually, for both lakes, early ice breakup is matched with late freeze-up. Conversely, late breakup is matched with early freeze-up. The magnitudes of midlake latent heat fluxes (evaporation) and sensible heat fluxes from Great Slave Lake are substantially larger than those from Great Bear Lake during their respective open-water periods. The hypothesis that because they are both large and deep, and are located in high latitudes, Great Slave Lake and Great Bear Lake will exhibit similar surface and near-surface climates that are typical of large lakes in the high latitudes proves invalid because their different hydrological systems impose very different thermodynamic regimes on the two lakes. Additionally, such an extensive north-flowing river system as the Mackenzie is subjected to latitudinally variable meteorological regimes that will differentially influence the hydrology and energy balance of these large lakes. Great Slave Lake is very responsive to climatic variability because of the relation between lake ice and absorbed solar radiation in the high sun season and we expect that Great Bear Lake will be affected in a similar fashion.