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Water filtration is a common strategy of water sanitation in resource-poor tropical settings. Here, we assessed the intermediate term effect of this preventive procedure including specific filter-related as well as general hygiene training on the molecular detection of enteric pathogens in stool samples from Colombian Indigenous people. From a total of 89 individuals from an Indigenous tribe called Wiwa, stool samples were assessed by real-time PCR for enteropathogenic microorganisms prior to the implementation of water filtration-based infection prevention. Three years after the onset of the preventive strategy, a follow-up assessment was performed. A significantly beneficial effect of water filtration could be shown for <i>Ascaris</i> spp. only (<i>p</i> = 0.035) and a tendency (<i>p</i> = 0.059) for <i>Hymenolepis nana</i>. No hints for effects on the gastrointestinal shedding of <i>Giardia duodenalis</i>, <i>Entamoeba histolytica</i>, <i>Cryptosporidium</i> spp., <i>Campylobacter</i> spp., <i>Shigella</i> spp./enteroinvasive <i>Escherichia coli</i>, <i>Necator americanus</i>, <i>Strongyloides stercoralis</i>, <i>Trichuris trichiura</i>, and <i>Taenia</i> spp. were seen. In conclusion, the study indicates that water filtration can only be an element of a multi-modal hygiene concept to reduce enteric pathogen carriage in inhabitants of resource-poor tropical settings in spite of tendencies of beneficial effects.