Flood events have increased significantly in recent decades as a result of climate change, causing severe damage to cultural heritage and, in particular, to archival and library collections. Paper-based materials contaminated by floodwaters and alluvial mud are subject not only to physical and biological deterioration, but also to potential hygienic and sanitary hazards associated with the persistence of human pathogens. Current emergency recovery strategies mainly focus on stabilizing materials through freezing, freeze-drying and mechanical cleaning, while health risk assessment is rarely addressed systematically. This study proposes an operational protocol based on microbiological indicators for assessing health risks during the remediation of flood-damaged archival and library materials. The protocol was applied to collections from the Aurelio Saffi Municipal Library of Forlì (Italy), severely affected by the Emilia-Romagna floods of May 2023. Indicators of recent and past faecal contamination, total microbial loads and se-lected viral targets were analysed before and after freeze-drying and mechanical cleaning. The results demonstrate a substantial reduction in faecal contamination fol-lowing freeze-drying, alongside the persistence of environmentally resistant microbial taxa. These findings highlight the need to integrate health risk considerations into con-servation recovery workflows to ensure the safety of conservation professionals and users of recovered heritage materials.