Access to basic water, sanitation and hygiene, waste management and environment cleaning (WASH) in healthcare facilities (HCFs) is critical for infection prevention and control. The WHO/UNICEF 2019 global baseline report on WASH in HCFs indicates that 51 and 23% of those in sub-Saharan Africa have basic access to water and sanitation, respectively. Guided by the political ecology of health theory, this research engaged with 13 key informants, 16 healthcare workers and 31 community members on their experiences on the implementation, use and management of WASH in HCFs. Interviews were conducted in one informal settlement and three rural dispensaries in Kisumu, Kenya from May to September 2019. Findings indicate improvement in water access, yet water quality and other WASH service components remain a challenge even in newly constructed maternity facilities, thus impacting local health promotion efforts. Institutional challenges such as limited financial resources and ecological factors like climate variability and disease outbreaks compromised WASH infrastructure and HCF resilience. To achieve Sustainable Development Goal 3, good health and well-being, as well as Sustainable Development Goal 6, clean water and sanitation, the prioritisation of WASH in HCFs is required at all levels, from the local to the global.