Background: Improved Water, Sanitation and Hygiene (WASH) in Healthcare facilities (HCFs) is of significant public health importance. It is associated with a reduction in the transmission of healthcare acquired infections (HAIs), increased trust and uptake of healthcare services, cost saving from infections averted, increased efficiency and improved staff morale. Despite these benefits, there is limited evidence on availability of WASH services in HCFs in the Greater Kampala Metropolitan Area (GKMA). This study assessed the availability of WASH services within HCFs in the GKMA in order to inform policy and WASH programming.Methods: A cross-sectional study was conducted in 60 HCFs. Availability of WASH services in the study HCFs was assessed using a validated WASH Conditions (WASHCon) tool comprising of structured interviews, HCF observations and microbial water quality analysis. Data were analysed using Stata 14 software and R software. Results: Overall, 84.5% (49/58) and 12.1% (7/58) of HCFs had limited and basic WASH service respectively. About 48.3% (28/58) had limited water service, 84.5% (49/58) had limited sanitation service, 50.0% (29/58) had limited environmental cleanliness service, 56.9% (33/58) had limited hand hygiene service, and 51.7% (30/58) had limited waste management service. About 94.4% of public HCFs had limited WASH service compared to only 68.2% of private not for profit facilities. More health centre IIIs, 92.5% and health centre IVs (85.7%) had limited WASH service compared to hospitals (54.5%).Conclusions: Our findings indicate that provision of water, sanitation, hand hygiene, environmental cleanliness, and health care waste management services within HCFs are largely hindered by structural and performance limitations. In spite of these limitations, it is evident that environmental cleanliness and treatment of infectious waste can be attained with better oversight and dedicated personnel. Attaining universal WASH coverage in HCFs will require deliberate and strategic investments across the different domains.