This study identified differences in the epidemiology of Giardia and Cryptosporidium infection for low-income populations residing on the United States-Mexico border. Participation included 77 households in three communities lacking adequate municipal water and sewage services. The household was the unit of analysis and sampling was from household biosolid waste from newly installed composting toilets. The proportion of households positive for Giardia and Cryptosporidium was high, 82% and 70%, respectively, and this was in contrast to the few households (14%) reporting at least one individual with diarrhea symptoms. This finding indicated that most of the participant families were chronically infected but asymptomatic. In the multivariate analysis, there was a statistically significant protective effect for Cryptosporidium in those households that purified drinking water but not for Giardia. Those households with children less than five years of age were 1.3 times at risk for Giardia infection. Our findings highlighted differences in the transmission mode of these two pathogens and underscore the need for interventions addressing hygiene, water supply, and sanitation.