In Nepal, the number of diarrhoea hospitalizations in all ages is seriously high. According to the World Health Organization, diarrheal diseases can be substantially prevented through safe drinking water sources. In the Kathmandu Valley, because of the shortage of piped water, local residents use alternative water sources, such as groundwater, jars and tanker water. However, these alternative water sources can be contaminated. This study aimed to clarify the relationship between diarrhoea risk and the combinations of drinking water sources. A survey using multiple questionnaires on diarrhoea occurrence, water sources and water treatment was conducted three time between 2015 and 2016. The odds ratios (ORs) of developing diarrhoea were significantly high for drinking jar (OR 6.1) and tanker water (OR 8.4) compared with not drinking. The combined drinking of jar and tanker water obtained the 1 log higher OR compared with drinking only piped water. Conversely, drinking groundwater had a low OR, implying that the residents refrained from drinking polluted groundwater. In conclusion, diarrhoea occurrence was related not only to the level of water contamination, but also to a behavioural factor, i.e. people’s careful management of the choice of multiple water sources.