This article shows how local knowledge may be valuably integrated into a scientific approach in the study of large and complex hydrological systems where data collection at high resolution is a challenge. This claim is supported through a study of the hydrodynamics of a large lake where qualitative data collected from professional fishers was combined with theory to develop a hypothesis that was then verified by numerical modeling. First the fishermen’s narratives were found to describe with accuracy internal wave motions that were evident in water column temperature records, which revealed their practical knowledge of the lake’s hydrodynamics. Second, local knowledge accounts emphasized the recurrent formation of mesoscale gyres and return flows in certain zones of the lake in stratified conditions, which did not appear in the physical data because of limitations of sampling resolution. We hypothesized that these features developed predominantly because of the interaction of wind-driven internal motions with the lake’s bathymetry, and the Earth’s rotation in the widest areas of the basin. Numerical simulation results corroborated the fishers’ descriptions of the flow paths and supported the hypothesis about their formation. We conclude that the collaboration between scientific and local knowledge groups, although an unusual approach for a physical discipline of the geosciences, is worth exploring in the pursuit of a more comprehensive understanding of complex geophysical systems such as large lakes.