Cyanobacterial blooms are a major nuisance in lakes and reservoirs worldwide due to their potential human health hazards, and hamper ecosystem services, including fishing and drinking water production. Frequent monitoring is mandatory for tracking their distribution in time and space in large water bodies, by probe measurements and sampling, and by remote sensing. Their combined use with a model makes it possible to go further into understanding cyanobacteria dynamics. The model helps interpret remotely-sensed surface distribution maps and the latter serve as model input. Here we adopt this approach to understand how cyanobacteria respond to water level fluctuations and to the thermal structure of reservoirs. In Karaoun Reservoir, the largest freshwater body in Lebanon, cyanobacteria have been strongly dominating phytoplankton since 2009. We applied the coupled hydrodynamic-ecological model Delft3D in combination with satellite temperature and chlorophyll images. Spring-autumn simulations of the water level and of water temperature were calibrated and validated with thermistor measurements, with minor discrepancies. The hydrodynamic model was further validated with remotely-sensed temperature maps (Landsat 8). The surface distribution of cyanobacteria was computed with a chlorophyll-a algorithm (Sentinel 2). We show the first results of the biological simulations and the comparison with chlorophyll satellite maps.