Thermal responses of inland waters to climate change varies on global and regional scales. The extent of warming is determined by system-specific characteristics such as fluvial input. Here we examine the impact of ongoing climate change on two alpine tributaries, the Aare River and the Rhône River, and their respective downstream peri-alpine lakes: Lake Biel and Lake Geneva. We propagate regional atmospheric temperature effects into river discharge projections. These, together with anthropogenic heat sources, are in turn incorporated into simple and efficient deterministic models that predict future water temperatures, river-borne suspended sediment concentration (SSC), lake stratification and river intrusion depth/volume in the lakes. Climate-induced shifts in river discharge regimes, including seasonal flow variations, act as positive and negative feedbacks in influencing river water temperature and SSC. Differences in temperature and heating regimes between rivers and lakes in turn result in large seasonal shifts in warming of downstream lakes. The extent of this repressive effect on warming is controlled by the lakes hydraulic residence time. Previous studies suggest that climate change will diminish deep-water oxygen renewal in lakes. We find that climate-related seasonal variations in river temperatures and SSC shift deep penetrating river intrusions from summer towards winter. Thus potentially counteracting the otherwise negative effects associated with climate change on deep-water oxygen content. Our findings provide a template for evaluating the response of similar hydrologic systems to on-going climate change.