Adequate and appropriate water, sanitation, and hygiene (WaSH) infrastructure is important for reducing pathogen exposures in developing communities. To improve the ability of field practitioners in optimizing WaSH infrastructure within communities, models can provide insight into the complex interactions among WaSH infrastructure, health outcomes, and geographies. This study investigated the significant correlations between WaSH infrastructure variables and three different health outcomes (diarrhea, environmental enteric dysfunction, and stunting) over five geographic regions within Guatemala. Exploratory structural equation modeling was used to build WaSH models from U.S. Agency for International Development (USAID) 2012 Food for Peace Survey data (n = 2,103). The models were then tested using USAID 2013 Western Highlands Integrated Program survey data collected from the same regions (n = 4,633). Our results support that significant WaSH infrastructure variables vary widely over health outcome and geographic region. Improved sanitation had the highest prevalence of significance among all models. The floor transmission route for pathogens was identified as significant across all geographies for child stunting. Additionally, commonalities in potential pathogen transmission routes were identified among environmentally similar geographies. Practitioners and policy makers must account for the specific geography and health outcome to identify which set of WaSH infrastructure interventions are most appropriate at the correct scale.