Waterborne diseases continue to plague the poorest people in low-income countries and are estimated to cause 4,600,000 acute incidents of diarrhea resulting in over 2,000 deaths daily. A major challenge is performing microbiology tests to monitor drinking water quality. Friends of the Old (FOTO) implemented a novel strategy using evidence-based microbiology to educate communities about the relationship between contaminated water and disease. Two commercially available tests for E.coli, adapted for fieldwork, provided easily interpreted results of contamination that correlate with WHO's disease risk categories. Simple and effective household water treatment options 'solar pasteurization and/or chlorination' were provided to all 14,400 families and 42 schools in Lower Nyakach, Kenya. From February to May, 2015, adjacent districts had serious cholera outbreaks, but in Lower Nyakach, where education and the use of chlorine were nearly universal, there were no cases of cholera and steadily decreasing rates of diarrhea. A cross-sectional study was conducted to verify self-reported water treatment practices with evidence-based microbiological testing. A random sample of 377 households revealed that 95% treat their water each and every time they collect. Microbiological verification found 96% of household safe water storage vessels were low risk compared to their very high risk source water. A strong association (p < 0.001) existed between the observed decrease in diarrhea trends from health facilities in Lower Nyakach and exposure to the novel training. The strategy used by FOTO could be replicated to empower communities worldwide to identify contaminated drinking water sources and to reduce the incidence of waterborne disease.