Introduction <p>Access to advanced water service in healthcare facilities is critical for ensuring patient safety, effective infection prevention and control and over all improves quality of service. However, in Ethiopia, particularly in Addis Ababa, the factors affecting access to advanced water service level in these facilities have not been thoroughly studied. Evidence regarding the determinants of advanced water service level is limited, and the WHO/UNICEF Joint Monitoring Programme (JMP) water service levels remain undocumented, leaving these determinants largely unknown. Therefore, this study aims to investigate factors affecting access to advanced water service level and examines seasonal variations in bacteriological water quality across healthcare facilities in Addis Ababa, Ethiopia.</p> Methods <p>A cross-sectional study was conducted among 382 healthcare facilities. From these facilities, 382 healthcare managers were interviewed, and 382 water samples were collected during both the wet and dry seasons. Multivariable logistic regression analysis was employed to examine the associations between the advanced water service level and its predictor variables.</p> Results <p>In this study, only 17.5% of healthcare facilities had advanced drinking water service, with significant seasonal variations in contamination levels, notably higher levels of E. coli, Enterococci, and total coliforms during the rainy season. The study’s findings revealed that healthcare facilities (HCFs) headed by male managers (adjusted odds ratio [AOR] = 0.33, 95% CI: 0.15–0.77), healthcare facilities led by managers with a first degree holder (AOR = 0.18, 95% CI: 0.04–0.75), healthcare facilities with water reservoirs located at ground surface (AOR = 0.03, 95% CI: 0.004–0.27), facilities with managers who received training on water safety plans (AOR = 4, 95% CI: 1.5–10.3), healthcare facilities conducting biannual drinking-water chlorination practice (AOR = 3.9, 95% CI:1.10–9.80), healthcare facilities with properly closed water reservoirs (AOR = 3.5, 95% CI: 1.24–9.90), healthcare facilities having water supply guidelines (AOR = 3.5, 95% CI: 1.23–10.12), HCFs having water treatment practice led by healthcare facility managers (AOR = 3.5, 95% CI: 1.20–10.70), and healthcare facilities with specific annual plans for water supply (AOR = 3.2, 95% CI: 1.1.32–7.86) were significantly associated with having advanced water service level.</p> Conclusion <p>This study highlights a concerning gap in providing advanced drinking water service level in healthcare facilities in Addis Ababa. This investigation identifies seasonal variations indicated higher levels of bacteriological contamination during the rainy season, particularly for E. coli, Enterococci, fecal coliforms, and total coliforms. Furthermore, this study identified key determinants affecting access to advanced water service. Therefore, these results underscore the urgent need for targeted interventions to enhance water infrastructure and management practices, thereby improving health outcomes and supporting the achievement of Sustainable Development Goals in healthcare settings.</p>