Hazard mapping for built heritage in seaports is essential due to the coexistence of natural events and anthropogenic activity-based. Hydro-geomorphological features and human-induced effects are diversely distributed, and both affect the preservation of valuable architectural, archaeological, industrial and infrastructural assets in administrative seaport boundaries. However, in the Italian context, the ongoing process of cataloguing heritage may limit the effectiveness of assessment and preservation strategies. This paper presents the first findings of hazard identification in Italian seaports as part of the national research project RE3WORK. The study focuses on the assessment of seaports’ susceptibility to natural and anthropogenic hazards to support the safe and sustainable reuse of their built heritage. By combining data on geographical location, port activities and systematic built heritage inventory, recurrences in natural and activity-induced hazards are identified at national scale, also thanks to national hazard maps and an international database of industrial-based hazards classification. As the main outcomes, flooding and explosion caused by industrial and civil navigation are identified as dominant hazards in seaports. A more detailed investigation is conducted at the regional scale, focusing on Apulia, South Italy, to examine site-specific hazard interactions. The analysis links the spatial distribution of built heritage with flood vulnerability and port activities, revealing local variations in hazard proneness. Findings highlight the predominant role of ship-related activities as explosion source, while also demonstrating the limitations of regional flood vulnerability mapping in effectively assessing built heritage exposure to natural hazards.