The understanding of physical dynamics is crucial to provide scientifically credible information on lake ecosystem management. We show how the combination of in situ observations, remote sensing data, and three-dimensional hydrodynamic (3D) numerical simulations is capable of resolving various spatiotemporal scales involved in lake dynamics. This combination is achieved through data assimilation (DA) and uncertainty quantification. In this study, we develop a flexible framework by incorporating DA into 3D hydrodynamic lake models. Using an ensemble Kalman filter, our approach accounts for model and observational uncertainties. We demonstrate the framework by assimilating in situ and satellite remote sensing temperature data into a 3D hydrodynamic model of Lake Geneva. Results show that DA effectively improves model performance over a broad range of spatiotemporal scales and physical processes. Overall, temperature errors have been reduced by 54 %. With a localization scheme, an ensemble size of 20 members is found to be sufficient to derive covariance matrices leading to satisfactory results. The entire framework has been developed with the goal of near-real-time operational systems (e.g., integration into meteolakes.ch).