Good sanitation and clean water are basic human rights yet they remain elusive to many rural communities in Sub-Saharan Africa (SSA). We carried out a cross sectional study to examine the impact of a four-year intervention aimed at improving access to water and sanitation and reducing waterborne disease, especially diarrhea in children under five years old. The study was carried out in April and May 2015 in Busangi, Chela and Ntobo wards of Kahama District of Tanzania. The interventions included education campaigns and improved water supply, and sanitation. The percentage of households (HHs) with access to water within 30 min increased from 19.2 to 48.9 and 17.6 to 27.3 in the wet and dry seasons, respectively. The percentage of HHs with hand washing facilities at the latrine increased from 0% to 13.2%. However, the incidence of diarrhea among children under five years increased over the intervention period, RR 2.91 95% CI 2.71–3.11, p < 0.0001. Availability of water alone may not influence the incidence of waterborne diseases. Factors such as water storage and usage, safe excreta disposal and other hygiene practices are critical for interventions negating the spread of water borne diseases. A model that articulates the extent to which these factors are helpful for such interventions should be explored.