Linkages between human, environmental, and animal health have been an increasingly important topic of geographical research in recent years. As more data become available for explicitly representing the geographies of these systems, and how they interact, geographers are playing an important role in shaping this research area. Whereas previously these linkages have been known, but rarely quantified, geographical data are now enabling surveillance of environmental changes, animal populations, and human populations in order to realize fine‐grained estimates of disease risk. In this paper, we consider the role of spatial data in this new research area, and characterize challenges of integrating and analyzing data across these domains. We explore these issues through three case studies into emerging zoonoses; avian influenza, Japanese encephalitis, and syndromic animal health surveillance. Issues of scale, availability and access, and linkage uncertainties are found to be key data issues. We anticipate these issues will be important research challenges for geographers working on zoonoses, and as part of multidisciplinary research teams. Finally, we suggest that geographers working in this area adopt the concept of vulnerability surveillance to address these issues and refocus research on vulnerable populations, interfaces, and areas.