Many healthcare facilities (HCFs) in rural areas of low- and middle-income countries (LMICs) lack safe, sufficient water supplies. We sought to understand which factors affect water quality in rural HCF in LMICs. In Ethiopia, Kenya, Rwanda, Uganda, Tanzania, Malawi, Mozambique, Zambia, Zimbabwe, Ghana, Mali, Niger, India, and Honduras, doctors and nurses were interviewed at 2,035 HCFs about their water source, staff training, and management practices. Water samples were also tested for E. coli contamination. We generated descriptive analyses and logistic regressions. Use of an improved water source (OR≈1.4), treatment of water (OR=1.26), management by a person with medical training (OR≈3.7), and presence of a protocol for operations and management (OR=1.29) were associated with safer water. These results suggest that in addition to addressing water source, storage, and treatment, stakeholders can also target organizational factors in order to improve water quality in HCFs.