Poor household drinking water quality and the early childhood diarrhea (ECD) and child growth stunting that result from it are a scourge that leads to the premature death of nearly 1.6 million children worldwide each year. Researchers have long studied the causes and prevention strategies of poor household water quality and ECD using intervention-control trials. Although the results of such trials can lead to useful information, they do not capture the complexity of this human/engineered/natural system. This dissertation reports on the development of an agent-based model (ABM) to study such a system in Limpopo, South Africa. This method proved to be an effective tool to develop a robust, quantitative understanding of the complex coliform bacteria transmission chain that leads to ECD and to investigate key mechanisms, risk factors, behaviors and intervention strategies to mitigate such transmission. This was achieved in three main parts. The first was an investigation of the sources and regrowth mechanisms of coliform bacteria as well as water, sanitation and hygiene (WASH) behavior in the communities. The second part was to use that information to inform the development of an ABM and use that ABM to explore the various risk factors a↵ecting the outcome variables of household water quality, ECD incidences and child growth stunting. Lastly, the ABM was used understand the long-term sustainability of a ceramic water filter (CWF) campaign using field data about longitudinal microbial e↵ectiveness.