Addressing climate change in Historical Urban Built Environments (HUBEs) presents a significant challenge, particularly in balancing adaptation and mitigation strategies for emergency situations while preserving heritage. The impact of climate change, particularly flooding, is exacerbated by the physical vulnerability and spatial complexity of HUBEs, along with the exposure and individual vulnerabilities of users (residents, visitors, outdoor/indoor occupants). These user-related factors exhibit spatiotemporal dynamics that vary depending on HUBE features and intended uses. Consequently, differential effects on flood risk arise, particularly across the HUBE network, i.e. open spaces (squares, streets), along with the surrounding built heritage. This work introduces and showcases the capabilities of an innovative, holistic flood risk assessment approach that integrates hazard, HUBEs’ vulnerability and user-related factors (e.g. number, type, location of users). Each risk factor is evaluated through simulations or rapid remote surveys, with a consensus model for Analytical Hierarchy Process used to derive an overall flood risk index, combining expert judgments. Finally, the approach associates the flood risk index with homogeneous open spaces in HUBEs, providing values for hourly intervals and key times of day. The method is applied to an urban district within the UNESCO area of Guimarães, Portugal. The results identify critical flood risk factors, including priority areas for vulnerability-reduction interventions and “hot-spots” influenced by the presence and type of users. This methodology offers a dynamic understanding of HUBEs and their risks, with the flood risk index serving as a tool for assessing the effectiveness of adaptation and mitigation strategies in future retrofitted scenarios.