The aim of this study was to compare the water quality of piped-to-plot source water with point-of-drinking water in the households of a low-income urban area in Bangladesh. A total of 430 low-income households and 78 communal sources connected to these households were selected from the East Arichpur area of Dhaka. The water samples were collected from point-of-drinking vessels (household members’ preferred drinking vessels i.e., a mug, glass, or bottle) in households and from linked sources at six-week intervals between September 2014 and December 2015. Water samples were processed using standard membrane filtration and culture methods to quantify E. coli. Analysis of paired data from source and point-of-drinking water collected on the same day showed that fecal contamination increased from source to point-of-drinking water in the households in 51% (626/1236) of samples. Comparison between bottles vs. other wide-mouth vessels (i.e., glasses, mugs, jugs) showed significantly lower odds (p = 0.000, OR = 0.58, (0.43–0.78)) of fecal contamination compared to other drinking vessels. The findings suggest that recontamination and post-treatment contamination at the point of drinking play a significant role in water contamination in households. Hygiene education efforts in the future should target the promotion of narrow-mouth drinking vessels to reduce contamination.