We introduced flocculant-disinfectant water treatment for 12 weeks in 103 households in Bangladesh to assess if drinking water would be chemically and microbiologically improved and the body burden of arsenic reduced. The median concentration of arsenic in tubewell water decreased by 88% after introduction of the flocculant-disinfectant from 136 microg/l at baseline to 16 (p < 0.001). The median concentration of total urinary arsenic decreased 42% from 385 microg/g creatinine at baseline to 225 microg/g creatinine after intervention (p < 0.001). Among 206 post-intervention drinking water samples that were reportedly treated on the date the sample was collected, 99 (48%) lacked residual free chlorine and 100 (49%) were contaminated with thermotolerant coliforms. The flocculant-disinfectant markedly reduced arsenic in drinking water, but treated drinking water was frequently contaminated with fecal organisms. The lesser reduction in urinary arsenic compared to water arsenic and the health consequences of this reduction require further research.