Combining field measurements, 3‐D numerical modeling, and Lagrangian particle tracking, we investigated wind‐driven, Ekman‐type coastal upwelling during the weakly stratified winter period 2017/2018 in Lake Geneva, Western Europe's largest lake (max. depth 309 m). Strong alongshore wind stress, persistent for more than 7 days, led to tilting and surfacing of the thermocline (initial depth 75–100 m). Observed nearshore temperatures dropped by 1°C and remained low for 10 days, with the lowest temperatures corresponding to those of hypolimnetic waters originating from 200 m depth. Nearshore current measurements at 30 m depth revealed dominant alongshore currents in the entire water column (maximum current speed 25 cm s−1) with episodic upslope transport of cold hypolimnetic waters in the lowest 10 m mainly during the first 3 days. The observed upwelling dynamics were well reproduced by a 3‐D hydrodynamic model (RMSE 0.2°C), whose results indicated that upwelled waters spread over approximately 10% of the lake's main basin surface area. Model‐based Lagrangian particle tracking confirmed that upwelled waters originated from far below the thermocline, that is, >150 m depth, and descended back to around 150–200 m depth over a wide area after wind stress ceased. Observational and particle tracking results suggest that wintertime coastal upwelling, which can occur several times during winter, is an overlooked transport process that is less sensitive to the effects of global warming than convective cooling. It can provide an effective but complex 3‐D pathway for deepwater renewal in Lake Geneva, and other large, deep lakes with a sufficiently long wind fetch.

The exchange flow between distinct sub-basins and large embayments is a ubiquitous feature of many lakes, for example,

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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.

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