Basin-scale quasi-geostrophic gyres are common features of large lakes subject to Coriolis force. Cyclonic gyres are often characterized by dome-shaped thermoclines that form due to pelagic upwelling which takes place in their center. At present, dynamics of pelagic upwelling in the Surface Mixed Layer (SML) of oceans and lakes are poorly documented. A unique combination of high-resolution 3D numerical modeling, satellite imagery and field observations allowed confirming for the first time in a lake, the existence of intense pelagic upwelling in the center of cyclonic gyres under strong shallow (summer) and weak deep (winter) stratified conditions/thermocline. Field observations in Lake Geneva revealed that surprisingly intense upwelling from the thermocline to the SML and even to the lake surface occurred as chimney-like structures of cold water within the SML, as confirmed by Advanced Very High-Resolution Radiometer data. Results of a calibrated 3D numerical model suggest that the classical Ekman pumping mechanism cannot explain such pelagic upwelling. Analysis of the contribution of various terms in the vertically-averaged momentum equation showed that the nonlinear (advective) term dominates, resulting in heterogeneous divergent flows within cyclonic gyres. The combination of nonlinear heterogeneous divergent flow and 3D ageostrophic strain caused by gyre distortion is responsible for the chimney-like upwelling in the SML. The potential impact of such pelagic upwelling on long-term observations at a measurement station in the center of Lake Geneva suggests that caution should be exercised when relying on limited (in space and/or time) profile measurements for monitoring and quantifying processes in large lakes.