Combining field observations, 3D hydrodynamic modeling, and particle tracking, we investigated wind-induced interbasin exchange between the Petit Lac (PL) (depth 75 m) and Grand Lac (GL) (depth 309 m) basins of Lake Geneva in early winter. Following a strong 2.5-day wind event, a two-layer flow field developed, where the downwind surface drift into the GL was balanced by counterflowing hypolimnetic currents into the PL. Velocities in both layers exceeded 20 cm/s, with the highest values (27 cm/s) found near the bottom. For 3.5 days, hypolimnetic temperatures at the confluence decreased to values found in the deep GL hypolimnion at 180-m depth. Approximately 1.5 days after the wind event ceased, currents reversed and upwelled waters returned into the deep GL hypolimnion. The Coriolis force strongly modified the interbasin exchange dynamics, which were well represented by the model. Particle tracking revealed a “current loop,” that is, water from below 150-m depth first upwelled into the PL, intruded approximately 10 km (half its length), and then descended back into the GL hypolimnion. Model results showed that the PL hypolimnetic volume doubled during the upwelling. Low model-based gradient Richardson numbers and temperature inversions in CTD profiles indicated turbulent mixing between the upwelled GL and surrounding PL waters. Our findings demonstrate that hypolimnetic upwelling between the two basins frequently occurs during winter and could potentially be an important, but as yet overlooked mechanism for hypolimnetic-epilimnetic exchange and deepwater renewal in Lake Geneva, and probably in other multi-depth basin lakes under similar wind conditions.