In large lakes subject to the Coriolis force, basin-scale gyres and mesoscale eddies, i.e. rotating coherent water masses, play a key role in spreading biochemical materials and energy throughout the lake. In order to assess the spatial and temporal extent of gyres and eddies, their dynamics and vertical structure, as well as to validate their prediction in numerical simulation results, detailed transect field observations are needed. However, at present it is difficult to forecast when and where such transect field observations should be taken. To overcome this problem, a novel procedure combining 3D numerical simulations, statistical analyses, and remote sensing data was developed that permits determination of the spatial and temporal patterns of basin-scale gyres during different seasons. The proposed gyre identification procedure consists of four steps: (i) data pre-processing, (ii) extracting dominant patterns using empirical orthogonal function (EOF) analysis of Okubo–Weiss parameter fields, (iii) defining the 3D structure of the gyre, and (iv) finding the correlation between the dominant gyre pattern and environmental forcing. The efficiency and robustness of the proposed procedure was validated in Lake Geneva. For the first time in a lake, detailed field evidence of the existence of basin-scale gyres and (sub)mesoscale eddies was provided by data collected along transects whose locations were predetermined by the proposed procedure. The close correspondence between field observations and detailed numerical results further confirmed the validity of the model for capturing large-scale current circulations as well as (sub)mesoscale eddies. The results also indicated that the horizontal gyre motion is mainly determined by wind stress, whereas the vertical current structure, which is influenced by the gyre flow field, primarily depends on thermocline depth and strength. The procedure can be applied to other large lakes and can be extended to the interaction of biological–chemical–physical processes.