Analysis of chlorophyll-a map from remote sensing satellite data (MERIS) showed a consistent low concentration biomass in the middle of Lake Geneva for about two weeks in autumn 2009. A three dimensional hydrodynamic model (Delft3D-flow) validated with temperature and currents field data partly explains the observed horizontal phytoplankton patchiness. Our analysis suggests that physical mesoscale processes and in particular the large gyre observed in the middle of Lake Geneva plays an important role in the spatial heterogeneity of the biomass. This study finally emphasizes the benefit of using jointly remote sensing data, field observation together with numerical model to provide a better understanding of lake ecosystems.