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Researchers have long studied the causes and prevention strategies of poor household water quality and early childhood diarrhea using intervention-control trials. Although the results of such trails can lead to useful information, they do not capture the complexity of this natural/engineered/social system. We report on the development of an agent-based model (ABM) to study such a system in Limpopo, South Africa. The study is based on four years of field data collection to accurately capture essential elements of the communities and their water contamination chain. An extensive analysis of those elements explored behaviors including water collection and treatment frequency as well as biofilm buildup in water storage containers, source water quality, and water container types. Results indicate that interventions must be optimally implemented in order to see significant reductions in early childhood diarrhea (ECD). Household boiling frequency, source water quality, water container type, and the biofilm layer contribution were deemed to have significant impacts on ECD. Furthermore, concurrently implemented highly effective interventions were shown to reduce diarrhea rates to very low levels even when other, less important practices were suboptimal. This technique can be used by a variety of stakeholders when designing interventions to reduce ECD incidences in similar settings.