Assessing water quality and identifying the potential source of contamination, by Sanitary inspections (SI), are essential to improve household drinking water quality. However, no study link the water quality at a point of use (POU), household level or point of collection (POC), and associated SI data in a medium resource setting using a Bayesian Belief Network (BBN) model. We collected water samples and applied an adapted SI at 328 POU and 265 related POC from a rural area in East Sumba, Indonesia. Fecal contamination was detected in 24.4 and 17.7% of 1 ml POC and POU samples, respectively. The BBN model showed that the effect of holistic—combined interventions to improve the water quality were larger compared to individual intervention. The water quality at the POU was strongly related to the water quality at the POC and the effect of household water treatment to improve the water quality was more prominent in the context of better sanitation and hygiene conditions. In addition, it was concluded that the inclusion of extra “external” variable (fullness level of water at storage), besides the standard SI variables, could improve the model’s performance in predicting the water quality at POU. Finally, the BBN approach proved to be able to illustrate the interdependencies between variables and to simulate the effect of the individual and combination of variables on the water quality.