Sustaining Water, Sanitation, and Hygiene (WASH), and Infection Prevention and Control (IPC) services in healthcare facilities (HCFs) remain a challenge in the developing world. This is largely attributable to ineffective management systems such as leadership, training, monitoring, financing and accountability, and operation and maintenance (O&M) for WASH and IPC. This study analysed management systems for the sustainability of WASH and IPC in HCFs in the Greater Kampala Metropolitan Area (GKMA), Uganda. A descriptive cross-sectional study was conducted in 59 HCFs. Data were obtained from HCF in-charges using the WASHCon tool. Indicators of sustainability across HCF level and ownership were compared using Chi-square tests, performed in Stata 14 statistical software. A p-value of less than 0.05 was considered significant. Less than half, 42.4% (25/59) of the HCFs had trained their staff on WASH issues, and 44.1% (26/59) had WASH and IPC guidelines. Nearly all, 91.2% (31/34) of the HCFs that needed new sinks, taps, or pipes could not afford them due to insufficient funds. The perceptions of in-charges that it was their responsibility: to ensure that staff receive training on WASH and IPC (p = 0.014); to oversee the O&M of WASH and IPC infrastructure (p = 0.005); and to sustain WASH and IPC infrastructure and behaviours (p = 0.014) varied by ownership of the HCF. Availability of written guidelines on WASH and IPC varied by level and ownership (p = 0.010). In this study, sub-optimal management systems for WASH and IPC were noted, and leadership, training and monitoring, financing, and accountability varied across level and ownership of the HCFs. Nonetheless, simple acts such as recognising the best performing staff in WASH and IPC can boost the morale of the staff. Also, there is a need for budget increments and functionalisation of the WASH and IPC committees in order to sustain recommended practices.