Mediterranean reservoirs are strategic water resources, particularly for drinking water supply. Hydrodynamics is one of the main drivers of their water quality. For management and planning purposes, an accurate understanding of their hydrological and thermal regime is required in particular for waters affected by harmful algal blooms. When in situ data are scarce and missing data interrupts the time-series, this limitation can be overcome by three-dimensional modelling coupled to satellite remote sensing images covering the whole surface domain. The objective of this work is to reproduce and understand the impact of hydrodynamics on cyanobacteria dynamics at Karaoun Reservoir, Lebanon through a 3D hydrodynamic model, Delft3D, in combination with satellite remote sensing images. Simulations of the water level and of water temperature during 2017 spring to autumn period were performed. The model results were compared with thermistor measurements recorded in 2017, and showed minor discrepancies. Water surface temperature was retrieved from Landsat 8 and corrected for atmospheric interferences. Remote sensing estimations of surface water temperature were compared to in situ observations and model simulations with overall good agreement. The model reproduced well water temperature, stratification, mixing processes and water level fluctuations. Simulations of cyanobacteria biomass in 2017 were also compared to field measurements and were found to be well represented. This study demonstrated the importance of satellite remote sensing as an additional source of data for integration into 3D modelling. Results will further help understand the driving factors of ecosystem dynamics at Karaoun Reservoir.