The management of groundwater quality is a critical issue in developing nations where sanitation and drinking-water targets are commonly addressed by facilitating access to groundwater, which is then managed as a common-pool resource. We investigate the quality of the shallow unconfined groundwater in Dili's alluvial fan system, which 50% of Dili's rapidly growing population access for all their water requirements. Using the basic chemical and microbiological analyses that are locally available (sulfate, total hardness, fluoride, manganese, iron, ammonia, nitrite, nitrate, totalColiform and E. Coli.) we show that the shallow wells commonly contain enhanced concentrations of dissolved solids and microbiological contaminants (Total coliform and E. Coli.), relative to deeper wells. Cool, shallow wells fare worse than warm equivalents. Elevated nitrate and nitrite pollution in the embassy district are tentatively attributed to affluence factors, such as lawn cultivation and water filtration equipment. Microbiological contamination, and associated manganese contamination of groundwater, mimic population patterns but are concentrated in the finer grained sediments of the small fans and low slope interdistributory areas. We suggest that rapid development and successful implementation of appropriate sanitation policy in Dili (and elsewhere) is required to address the problematic features of the shallow groundwater system. Success will be predicated on 1) the establishment of baseline data, and 2) development of a systems-thinking approach to holistic water resource management. Any such program must engage with community leadership and water politics, and with the full, presently poorly understood, cohort of water-related service providers and NGOs operating in Timor-Leste.