In large lakes, basin-scale gyres and submesoscale eddies, i.e., rotating coherent water masses, play a key role in spreading biochemical materials and energy throughout the basin, thereby significantly impacting water quality. Due to their transient and spatially heterogeneous nature, detailed field measurements of these flow features are challenging and thus scarce. However, such measurements are crucial to investigate the spatiotemporal extent and dynamics of basin-scale gyres and submesoscale eddies, assess ecological implications, and validate numerical simulation results. Combining extensive field observations, three-dimensional (3D) numerical simulations, remote sensing data and statistical analyses, this thesis explores the dynamics of basin-scales gyres and submesoscale eddies in Lake Geneva, unraveling the implications for water quality heterogeneity and existing lake monitoring strategies. First, a novel framework is developed that permits study the spatiotemporal characteristics of gyres/eddies during different seasons by allowing efficient design of field sampling strategies with unprecedented precision in time and space. Building on this novel framework, the existence of submesoscale filaments caused by large-scale gyres is demonstrated for the first time in a lake. Then, the dynamics of pelagic upwelling within a cyclonic gyre in Lake Geneva are investigated. Finally, the spatial heterogeneity of water quality parameters caused by (sub)mesoscale flow features is revealed. Submesoscale filaments, well-documented in the ocean but poorly understood in lakes, are spatially-elongated bands often observed within large-scale gyres/eddies. Submesoscale currents have horizontal scales of 0.1–10 km, lifetimes of hours to days, and are characterized by Rossby and Richardson numbers both of O(1). Measurements in Lake Geneva demonstrate that submesoscale, cold-water filaments are formed at the edges and in the center of cyclonic large-scale gyres above the thermocline during summertime, confirming 3D numerical modeling results and remote sensing data. Field observations in Lake Geneva revealed that surprisingly intense submesoscale upwelling from the thermocline to the Surface Mixed Layer (SML) and even the lake surface occurred as chimney-like structures of cold water within the SML, as confirmed by Advanced Very High-Resolution Radiometer data. The potential impact of such pelagic upwelling on a long-term 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. The role of mesoscale circulations in determining the spatial heterogeneity of water quality parameters remains poorly understood in large lakes. This thesis provides unparalleled evidence of dissolved oxygen (DO) variability caused by cyclonic gyres (CGs), anticyclonic gyres (AGs), submesoscale eddies, and filaments in both weak (fall) and strong (summer) thermal stratification conditions. In the presence of CGs, AGs, and submesoscale flows, significant lateral variations in DO, mixed layer depth, and metalimnion depth were observed. Such spatial variability of water quality parameters induced by (sub)mesoscale circulations challenges classical one-dimensional (1D) long-term monitoring programs for quantifying physical and biological processes in large lakes.