Access to safe drinking water has been an important national goal in Bangladesh and other developing countries. While Bangladesh has almost achieved accepted bacteriological drinking water standards for water supply, high rates of diarrheal disease morbidity indicate that pathogen transmission continues through water supply chain (and other modes). This paper investigates the association between water quality and selected management practices by users at both the supply and household levels in rural Bangladesh. Two hundred and seventy tube-well water samples and 300 water samples from household storage containers were tested for fecal coliform (FC) concentrations over three surveys (during different seasons). The tube-well water samples were tested for arsenic concentration during the first survey. Overall, the FC was low (the median value ranged from 0 to 4 cfu/100 ml) in water at the supply point (tube-well water samples) but significantly higher in water samples stored in households. At the supply point, 61% of tube-well water samples met the Bangladesh and WHO standards of FC; however, only 37% of stored water samples met the standards during the first survey. When arsenic contamination was also taken into account, only 52% of the samples met both the minimum microbiological and arsenic content standards of safety. The contamination rate for water samples from covered household storage containers was significantly lower than that of uncovered containers. The rate of water contamination in storage containers was highest during the February–May period. It is shown that safe drinking water was achieved by a combination of a protected and high quality source at the initial point and maintaining quality from the initial supply (source) point through to final consumption. It is recommended that the government and other relevant actors in Bangladesh establish a comprehensive drinking water system that integrates water supply, quality, handling and related educational programs in order to ensure the safety of drinking water supplies.