Diarrhea is still a health problem in the community, due to it's high level of morbidity and mortality, especially among under five children. Based on Baseline Health Research (Riskesdas) 2013, DKI Jakarta Province had good coverage of improved water access, sanitation, and personal hygiene behavior (PHBS), however, the prevalence of diarrhea was still high, and ranked in the top five for children under five in Indonesia. The aim of this study was to determine the effect of drinking water access to diarrhea among children under five adjusted by source of drinking water, sanitation, and mother's handwashing behavior in DKI Jakarta. This study was a cross-sectional study with children under five of age in Riskesdas 2013 as unit of analysis. Data were analyzed by logistic regression to test the relationship between drinking water source as the main independent variable and diarrhea of children as dependent variable adjusted by other variables as confounders. The results showed that unimproved drinking water source affected diarrhea among children under five (p = 0.003) with OR(95%CI)=1.9(1.26–2.89) adjusted by sanitation and mother's handwashing behavior. There were 47.1% households of children under five who suffered from diarrhea used drinking water refill. Therefore, we suggested that the households should process the drinking water refill before consume and the local health authority should make routine supervision to the depot of drinking water refill.