The socio-political context of modern environmental health disasters tends to be defined as being outside the scope of official public health and epidemiological investigations into the causes of such disasters. On the other hand, popular accounts of these disasters tend to focus exclusively on the role of particular individuals and/or political actors, while minimizing the role of ecological factors. It is argued that an exclusive focus on either set of causal factors gives an incomplete or distorted picture of the origins of an environmental health disaster. In this paper, a socio-ecological analysis is developed to demonstrate how the largest outbreak of waterborne E. coli O157:H7 in Canadian history was the emergent product of a complex interplay and intertwining of social and ecological processes. The socio-ecological autopsy approach that is developed here traces the social and ecological chain of events that ultimately led to the outbreak and demonstrates, in particular, the need for investigative analysis to focus on the socio-ecological "incubation" of an environmental health disaster. Drawing from both the social sciences (particularly, the sociology of disasters and organizational sociology), and from the ecological sciences (particularly disease ecology), the analysis developed here responds to the call for the application of a more transdisciplinary approach to the study of contemporary environmental health problems.