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Although vertical mode‐one (V1) Kelvin waves are known to play an important role in nearshore dynamics of large lakes, observations of vertical mode‐two (V2) Kelvin waves are scarce, and their characteristics and significance are largely unknown. Combining field observations, 3D hydrodynamic modeling, and particle tracking, we demonstrate that previously undetected V2 Kelvin waves are common in Lake Geneva (Switzerland/France) during summer. V2 Kelvin waves with a 5‐d period persisted for over one month in 2021 and 2022. Modeling revealed a complex, spatially heterogeneous vertical structure. Since the lower nodal line depth varied from ∼150 to 200 m near the shores to ∼75 m in the lake center, V2 Kelvin waves were restricted to the deep eastern basin (maximum depth 309 m), and nearshore current profiles observed at ∼110‐m depth did not show the typical V2 modal structure. The waves produced large vertical isotherm displacements (∼25 m) and strong currents (∼28 cm s−1) in the nearshore thermocline and induced alongshore transport over nearly half the basin length. Currents were strongest ∼1 km from shore and decreased exponentially toward the lake center. Our findings explain why previous studies in Lake Geneva's nearshore regions (out to ∼75‐m depth) only detected V1 Kelvin waves and no V2 Kelvin waves. Modeling revealed that V2 Kelvin waves are consistently excited under typical summer stratification and wind forcing conditions. Our results suggest that these waves occur in other large deep lakes having a Burger number , with important implications for the transport and dispersion of sediments, nutrients, and pollutants.