Quantum yield of fluorescence (ϕF) is key to interpret remote measurements of sun-induced fluorescence (SIF), and whether the SIF signal is governed by photochemical quenching (PQ) or non-photochemical quenching (NPQ). Disentangling PQ from NPQ allows using SIF estimates in various applications in aquatic optics. However, obtaining ϕF is challenging due to its high temporal and physiological variability, and the combined measurements needed to enclose all relevant optical paths. In inland waters, this type of data is scarce and information on diurnal and seasonal ϕF dynamics are almost unknown. Using an autonomous hyperspectral Thetis profiler in Lake Geneva, we demonstrate how to estimate ϕF using an ensemble of in-situ measurements acquired between 2018 to 2021. We use vertical and temporal changes in retrieved ϕF to determine NPQ and PQ conditions. We observed NPQ in 36% of the total daytime profiles used in the ϕF analysis. While downwelling irradiance is a significant contributor to ϕF, its role cannot be easily interpreted. Other factors such as phytoplankton photoregulation and assemblages also likely play significant roles in quenching mechanisms. We conclude that an adapted approach exploiting in-situ data is suitable to determine diurnal and seasonal NPQ occurrence, and helps develop future remote sensing algorithms.