There is a critical need for safe water in healthcare facilities (HCF) in low-income countries. HCF rely on water supplies that may require additional on-site treatment, and need sustainable technologies that can deliver sufficient quantities of water. Water treatment systems (WTS) that utilize ultrafiltration membranes for water treatment can be a useful technology in low-income countries, but studies have not systematically examined the feasibility of this technology in low-income settings. We monitored 22 months of operation of 10 WTS, including pre-filtration, membrane ultrafiltration, and chlorine residual disinfection that were donated to and operated by rural HCF in Rwanda. The systems were fully operational for 74% of the observation period. The most frequent reasons for interruption were water shortage (8%) and failure of the chlorination mechanism (7%). When systems were operational, 98% of water samples collected from the HCF taps met World Health Organization (WHO) guidelines for microbiological water quality. Water quality deteriorated during treatment interruptions and when water was stored in containers. Sustained performance of the systems depended primarily on organizational factors: the ability of the HCF technician to perform routine servicing and repairs, and environmental factors: water and power availability and procurement of materials, including chlorine and replacement parts in Rwanda.