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Remote sensing helps foster our understanding of inland water processes allowing a synoptic view of water quality parameters. In the context of global monitoring of inland waters, we demonstrate the benefit of combining in-situ water analysis, hydrodynamic modelling and remote sensing for investigating biogeochemical processes. This methodology has the potential to be used at global scales. We take the example of four Landsat-8 scenes acquired by the OLI sensor and MODIS-Aqua imagery over Lake Geneva (France—Switzerland) from spring to early summer 2014. Remotely sensed data suggest a strong temporal and spatial variability during this period. We show that combining the complementary spatial, spectral and temporal resolutions of these sensors allows for a comprehensive characterization of estuarine, littoral and pelagic near-surface features. Moreover, by combining in-situ measurements, biogeochemical analysis and hydrodynamic modelling with remote sensing data, we can link these features to river intrusion and calcite precipitation processes, which regularly occur in late spring or early summer. In this context, we propose a procedure that can be used to monitor whiting events in temperate lakes worldwide.