Background: To design the most appropriate interventions to improve water quality and supply, information is needed to assess water contamination in a variety of community settings, including those that rely primarily on unimproved surface sources of drinking water. Objectives: We explored the role of initial source water conditions as well as household factors in determining household water quality, and how levels of contamination of drinking water change over time, in a rural setting in northern coastal Ecuador. Methods We sampled source waters concurrently with water collection by household members and followed this water over time, comparing Escherichia coli and enterococci concentrations in water stored in households with water stored under controlled conditions. Results: We observed significant natural attenuation of indicator organisms in control containers and significant, although less pronounced, reductions of indicators between the source of drinking water and its point of use through the third day of sampling. These reductions were followed by recontamination in approximately half of the households. Conclusions: Water quality improved after water was transferred from the source to household storage containers, but then declined because of recontamination in the home. Our experimental design allowed us to observe these dynamics by controlling for initial source water quality and following changes in water quality over time. These data, because of our controlled experimental design, may explain why recontamination has been reported in the literature as less prominent in areas or households with highly contaminated source waters. Our results also suggest that efforts to improve source water quality and sanitation remain important.