This study aimed to quantify the inequalities and identify the associated factors of the UN sustainable development goal (SDG) targets in relation to safe drinking water. The concentration of the gut bacterium Escherichia coli in drinking water at the point of use (POU) and other information were extracted from the latest wave of the nationally representative Bangladesh Multiple Indicator Cluster Survey (MICS 2019). Bivariate and multivariable multinomial logistic regression models were used to identify potential predictors of contamination, whereas, classification trees were used to determine specific combinations of background characteristics with significantly higher rates of contamination. A higher risk of contamination from drinking water was observed for households categorized as middle or low wealth who collected water from sources with higher concentrations of E. coli. Treatment of drinking water significantly reduced the risk of higher levels of contamination, whereas owning a pet was significantly associated with recontamination. Regional differences in the concentrations of E. coli present in drinking water were also observed. Interventions in relation to water sources should emphasize reducing the level of E. coli contamination. Our results may help in developing effective policies for reducing diarrheal diseases by reducing water contamination risks.