This study examines the inter-annual variability of the thermal regime of two lakes, Quesnel Lake a very long residence-time lake and Kamloops Lake a short residence-time river-dominated lake. The changes are compared to local climate conditions as well as inter-annual variability associated with the El Nino Southern Oscillation (ENSO). Observations include that higher air temperatures in El Nino years are associated with higher surface water temperature, as well as earlier onset and longer duration of summer stratification. Observed lake heat content calculated from temperature profiles balanced well with the sum of heat fluxes calculated from meteorological data. Results indicate differences in the importance of heat flux components to the heat budgets of these lakes especially the river throughflow in Kamloops Lake. Since climate projections indicate more warming for this region the different potential impacts to the thermal regime of these lakes should be considered in environmental and resource management decisions.