The Encyclopaedia Cloacae is a novel and centralised digital platform designed to support and advance wastewater-based epidemiology (WBE) by cataloguing pathogens detectable in wastewater and their relevance to public health surveillance. The platform is hosted on the EU Wastewater Observatory for Public Health (EU4S) website, where it is populated with peer-reviewed research through a structured workflow under harmonised criteria which address the presence of pathogens in human excreta, detectability in wastewater, and integration into public health systems. This tri-criteria approach ensures that the database is both scientifically robust and operationally actionable. Complemented by the Visualising the Invisible dashboard, the platform offers geospatial insights into global WBE research activity. By consolidating peer-reviewed evidence on pathogen detectability in wastewater and human excreta, the Encyclopaedia Cloacae enables early detection of infectious diseases, whether already known or newly emerging. The continuously updated repository and geospatial dashboards help to identify surveillance gaps and research hotspots, to support timely public health responses, enhance pandemic preparedness, and strengthen global health security. In addition, it supports One Health strategies, connecting the health of humans, animals, and the shared environment. This article outlines the platform’s architecture, data curation methodology, and future directions, including automation and expansion to encompass broader health determinants such as antimicrobial resistance and chemical hazards.