Land transformation can have cascading effects on hydrology, water quality, and human users of water resources, with serious implications for human health. An interdisciplinary analysis is presented, whereby remote-sensing data of changing land use and cover are related to surface hydrology and microbial contamination in domestic use areas of three indigenous Maya communities in Belize, Central America. We asked whether a departure from traditional land-use patterns toward intensified use led to consequences for hydrology and microbial contamination of drinking water, and investigated how social factors in the three study communities may act to ameliorate human health risks associated with water contamination. We showed that a departure from traditional land use to more intensive cultivation and grazing led to significantly increased surface water runoff, and intensified microbial contamination of surface water sources sometimes used for drinking. Results further suggested that groundwater contamination was widespread regardless of land cover, due to the widespread presence of pit latrines, pigs, and cows on the landscape, and that human users were consistently subject to health risks from potential pathogens as a result. Given that both surface and groundwater resources were found to be contaminated, it is important that water distribution systems (piped water from tanks; shallow and deep wells) be monitored for Escherichia coli and treated when necessary to reduce or eliminate contaminants and protect public health. Results of interviews suggested that strengthened capacity within the communities to monitor and treat centralized drinking water sources and increase water treatment at the point of use could lead to reduced risk to water consumers.