Water sanitation and hygiene-related disease and malnutrition are a high priority in developing countries, including Rwanda. Interventions that can trigger and sustain household-level behavioral change and practice are needed. A case-control study was conducted to assess the potential of the Community Health Club (CHC) intervention, which consisted of village-based health education on water sanitation, hygiene, nutrition, and monitoring of households’ practices to reduce water sanitation and hygiene-related disease and malnutrition. The study targeted one village which had been exposed to the CHC. As a control, one village was picked from among villages that had not been exposed to CHC intervention. The two villages were in the catchment area of the Nyabitimbo Health Center and shared the same water sources for domestic use in the Rusizi district in Rwanda. The study examined the prevalence of intestinal worms, diarrhea, and malnutrition among children under 5 years old as recorded in the registries of Nyabitimbo Health Center for the period of the study, 2013–2015. The study results revealed that the CHC intervention was associated with a reduction of intestinal worms, diarrhea, and malnutrition, but the results were only statistically significant for intestinal worms and malnutrition. The present study, being exploratory, can serve for planning and practice purposes at the specific study area.