Provision of basic water, sanitation, and hygiene (WASH) services in health-care facilities is gaining increased attention, given growing acceptance of its importance to the maternal and newborn quality of care agenda and the universal health coverage framework. Adopting and contextualizing an emerging World Health Organization/United Nations Children's Fund Joint Program Monitoring service ladder approach to national data collected in 2010/2011, we estimated the national coverage of primary health centers (PHCs) (N = 8,831), auxiliary PHCs (N = 22,853), village health posts (N = 28,692), and village maternity clinics (N = 14,396) with basic WASH services in Indonesia as part of a Sustainable Development Goal baseline assessment. One quarter of PHCs did not have access to a combination of basic water and sanitation (WatSan) services (23.6%) with significant regional variation (10.6-59.8%), whereas more than two-third of PHCs (72.0%) lacked handwashing facility with soap in all three locations (general consulting room, immunization room, and delivery room). More than a half of the three lower health service level facility types lacked basic WatSan services. National health facility monitoring systems need to be urgently strengthened for tracking the progress and addressing gaps in basic WASH services in health facilities in Indonesia.