Water scarcity is a major issue in the Kathmandu Valley. Also, from a health perspective, it is important to evaluate the relationship between the quantity and quality of available water. In this study, we identified the water source used, and its availability and quality at the source and point of use. This was done by conducting a questionnaire survey and measuring the level of indicator bacteria and free residual chlorine in domestic water sampled at households. The results showed that most households used mixed water sources, with piped water being preferred for consumption. Nonparametric statistical tests showed that the total coliform was significantly high in source water with a longer supply interval and also high in stored water. In addition, but not of statistical significance, Escherichia coli was mostly detected in source water with a longer supply interval and also in stored water. In contrast, the proportion of samples with free residual chlorine was lower in water with a longer supply interval. Partial correlations showed that a longer cleaning interval of water storage vessels was associated with lower water availability and might lead to contamination of stored water. Therefore, safe storage of water should be promoted at the household level, and water supply services should be improved at the regional scale.