Assessment of water, sanitation, and hygiene (WASH) facilities in Primary Healthcare Centres (PHCs) and water source quality in parts of Southwestern Nigeria was conducted. Sixty-one PHCs in urban and rural areas were selected using a stratified random sampling technique. A WASH profile of the PHCs was conducted based on the water source type, type of toilet facilities, and handwashing practice using the Joint Monitoring Programme service ladder for monitoring WASH services in healthcare facilities. Water sources were tested for pH, electrical conductivity, total dissolved solids, turbidity, chloride, nitrate, and E. coli. Boreholes and hand-dug wells are the most prevalent water source type, and flush toilets and pit latrines are the major types of toilet facilities used. All but two PHCs engaged in handwashing practices. Water quality analysis results showed that chloride, nitrate, and turbidity were within the WHO drinking-water standards. Poor water quality and sanitation practices could expose health staff and patients to healthcare-associated infections. The study recommends the construction of safe, secure and accessible water sources and toilet facilities, provision of water treatment facilities, and the training of staff and patients on the significance of handwashing practices.