Early life pathogenic and nutritional environments impact health over the life course by training the immune system to adapt to local microbial conditions and developing metabolic trajectories based on resource availability. Exposure to environmental microbes during childhood, common throughout evolutionary history, can provide immunoregulatory properties that strengthen the immune system’s ability to resolve inflammation. In populations with childhood undernutrition, pathogenic exposures due to unsanitary living conditions can cause chronic intestinal inflammation. This condition, known as environmental enteric dysfunction, allows for microbes to enter the blood causing endotoxemia and systemic infection. Chronic immunostimulation during childhood is energetically demanding and often results in growth deficits. This dissertation uses the emerging field of the gut microbiome as pathway to investigate the early life effects of overnutrition and poor water quality on childhood intestinal health and immune function in Galápagos, Ecuador. Residents of San Cristóbal are unfortunately experiencing a dual burden of both increasing rates of obesity, coupled with persistent rates of infectious disease. Data was collected from 169 children aged two to ten and their 119 mothers. Interviews obtained information concerning household water use and sanitation practices, and children’s hygiene behaviors, illness histories and diets. Household water samples were collected to quantify fecal pathogens. Anthropometric assessments provided indicators of nutritional status. Blood spots were measured for immune biomarkers and fecal samples were collected to examine gut microbial compositions. Novel hypotheses are tested for the dual burden environment that examine the relationship between pathogenic and obesogenic factors on inflammation, endotoxemia and gut microbial composition, and provide insight into the early life health impacts of the dual burden environment on childhood intestinal health and immune function. The significant of this research is that even in the context of a pro-inflammatory state, driven by overweight and obesity, early life exposure to Escherichia coli contaminated water, which does not result in diarrhea, can provide an immunoregulatory effect among children in Galápagos. Identifying gut microbial symbiosis as a possible mechanism underlying this protective effect is an original contribution to the evolutionary “old friends” hypothesis and is of particular importance to public health research on environmental enteric dysfunction.