The focus of the present study was to assess the quality of different drinking water sources, impacts of poor water quality on human health, and to apportion pollution source(s) of the district Bajaur, Pakistan. Drinking water samples (n = 331) were randomly collected from springs, hand pumps, open wells, and tube wells and analyzed for physicochemical parameters including toxic elements, and bacteriological contamination (i.e., Escherichia coli). Furthermore, a questionnaire survey was conducted to record the cases of waterborne diseases in the study area. The results showed that total suspended solids and bacteriological contamination exceeded the permissible limits of the WHO in all four of the water sources. Among the potentially toxic elements, Cd, Pb, and Mn were above the permissible limits of the WHO in some samples. The hazard index for spring water was found to exceed the toxicity level (i.e., HI > 1) set by US EPA for both adults and children, while the sources from hand pumps, open wells, and tube wells were within the safe limit. The order for the overall safety level for water quality in the study area was tube wells > open wells > hand pumps > springs. The pollution source apportionment statistics revealed that both geogenic and anthropogenic activities are the sources of drinking water contamination. The results of the questionnaire survey indicated that reports of waterborne diseases were highest in respondents who took their drinking water from springs, whereas reports of diseases were moderate in respondents taking their water from open wells and hand pumps and lowest in respondents taking their water from tube wells. Based on the findings of the study, the tube well source of water is recommended for drinking water purposes.