Preserving cultural heritage sites demands risk management strategies that capture site-specific vulnerabilities at fine spatial resolutions. The present study introduces a novel framework for flood risk assessments that bridges large-scale hydrological modeling and sub-meter-level hydraulic simulations to provide enhanced insights into potential impacts. Our approach employs state-of-the-art Rain-on-Grid (RoG) hydraulic simulations, targeted field data collection, and high-resolution geometric documentation using UAV imagery and GNSS ground control points to account for detailed terrain characteristics. Within the scope of the Horizon Europe TRIQUETRA Project, we apply this framework to the Apollo temple in the archaeological site of Kolona on Aegina Island, Greece. A total of 945 vertical and 4900 oblique UAV images were processed following a multi-image photogrammetric workflow, to produce a digital surface model with a resolution of 1 cm. We then use this data to set up the RoG model and to analyze flood scenarios for various return periods to obtain sub-meter-level hydraulic parameters and evaluate how the site’s vulnerability to flood intrusion might change if its existing wall obstructions were to be extended. The proposed methodology offers a robust means to extract high-resolution boundary conditions for advanced computational fluid dynamics simulations. Using our multi-scale workflow, relevant stakeholders can enhance their data-driven decision-making for cultural heritage protection and preservation purposes. Acknowledgments: This work is based on procedures and tasks implemented within the project “Toolbox for assessing and mitigating Climate Change risks and natural hazards threatening cultural heritage—TRIQUETRA”, which is a Project funded by the EU HE research and innovation program under GA No. 101094818.