Although the African Great Lakes are important regulators for the East African climate, their influence on atmospheric dynamics and the regional hydrological cycle remains poorly understood. This study aims to assess this impact by comparing a regional climate model simulation that resolves individual lakes and explicitly computes lake temperatures to a simulation without lakes. The Consortium for Small-Scale Modelling model in climate mode (COSMO-CLM) coupled to the Freshwater Lake model (FLake) and Community Land Model (CLM) is used to dynamically downscale a simulation from the African Coordinated Regional Downscaling Experiment (CORDEX-Africa) to 7-km grid spacing for the period of 1999–2008. Evaluation of the model reveals good performance compared to both in situ and satellite observations, especially for spatiotemporal variability of lake surface temperatures (0.68-K bias), and precipitation (−116 mm yr−1or 8% bias). Model integrations indicate that the four major African Great Lakes almost double the annual precipitation amounts over their surface but hardly exert any influence on precipitation beyond their shores. Except for Lake Kivu, the largest lakes also cool the annual near-surface air by −0.6 to −0.9 K on average, this time with pronounced downwind influence. The lake-induced cooling happens during daytime, when the lakes absorb incoming solar radiation and inhibit upward turbulent heat transport. At night, when this heat is released, the lakes warm the near-surface air. Furthermore, Lake Victoria has a profound influence on atmospheric dynamics and stability, as it induces circular airflow with over-lake convective inhibition during daytime and the reversed pattern at night. Overall, this study shows the added value of resolving individual lakes and realistically representing lake surface temperatures for climate studies in this region.