The influence of three-dimensional (3D) hydrodynamic processes, in particular that of mesoscale cyclonic (CEs) and anticyclonic eddies (ACEs), on water quality in lakes is largely unexplored. In this study, high-resolution field measurements based on 3D forecasting simulations allowed examination of how mesoscale eddies modulate the spatial distribution of key water quality parameters such as dissolved oxygen (DO), conductivity, and thermal stratification in Lake Geneva. The analysis focuses on periods of strong (summer) and weak (fall) thermal stratification. Results reveal that the interplay between simultaneously occurring CEs and ACEs (diameters ~ 10 km) causes lateral variability in water quality by regulating the strength, the extent, and the shape of the metalimnion, a critical stratification interface. Compared to profiles taken at a station outside these eddies, CEs are characterized by higher DO concentrations, a shallower mixed layer, and a thicker metalimnion, whereas ACEs exhibit opposite trends. Within the mixed layer and metalimnion, DO production in summer and consumption in the fall occur across a wider depth range in the thicker metalimnion induced by CEs, whereas ACEs compress the metalimnion and limit vertical exchange. It is demonstrated that, depending on the season, extreme values of vertical DO gradients are primarily controlled by CEs or ACEs, which influence the depth distribution and intensity of biological processes, with potential implications for lake ecosystem dynamics.