This study examines how the locational characteristics of heritage sites influence their current flood risk in an urban environment under changing climate conditions. We studied 1620 heritage sites in the highly urbanized environment of Seoul, Korea; the study first quantified the flood risk of heritage sites, considering the topography and hydrological environment under 10-, 30-, and 50-year return periods of extreme precipitation scenarios. Terrain analyses were then applied to examine the physical locational characteristics of heritage sites related to flood susceptibility, with a literature review on the historical origin and human factors of each site. The evaluation of the location conditions of at-risk sites and their relationship with the construction period and type of heritage sites was conducted. The results show that the physical, political, economic, social, and cultural determinants of location varied depending on the construction period and heritage type, leading to the present spatial distribution of heritage sites. Specific sites in topographical knickpoints and lowlands near streams, which face additional hydraulic pressure and drainage issues from urban development, showed particularly high flood risks. By examining the interplay between historical, physical, and urban development factors, the research provides a holistic understanding of flood risks, essential for sustainable conservation strategies.