Abstract: Objective To investigate the hygiene status of water supply systems in self-built facilities within a region located in southeast China, and conduct a comprehensive analysis to provide scientific evidence for authorities to enhance drinking water hygiene management and improve water quality. Methods From June to July 2024, a hygienic survey was conducted on 58 self-built water supply facilities within a region located in southeast China. One terminal tap water sample was collected from each facility and tested for 27 water quality parameters. The results were evaluated according to the Standards for Drinking Water Quality (GB 5749-2022). Factors influencing the water quality of these self-built water supply systems were analyzed. Results A total of 58 self-built facilities for water supply were surveyed. The main type of water source was groundwater (65.52%). The surrounding topography was mainly mountainous (44.83%). The inner wall materials of water storage and supply facilities were mainly cement (68.97%). Water purification was performed in 39.66% of facilities. All the terminal water supplied by self-built facilities lacked disinfection measures. Water source protection measures were implemented in 70.69% of facilities. Hygiene management protocols and records were established in 12.07% and 15.52% of facilities, respectively. Routine water quality testing was performed in 50.00% of facilities. The qualified rate of the tested water samples was 24.14%. The primary indicators failing to meet standards were total coliforms, total bacterial count, and Escherichia coli, which were unqualified in 65.52%, 46.55%, and 31.03% of facilities, respectively. Multivariable logistic regression analysis showed that, compared with facilities without any water treatment measures, the water samples from facilities with filtration and installation of water purification devices had higher qualified rates, with odds ratios (ORs) (95% confidence intervals CIs) of 0.164 (0.030, 0.903) and 0.016 (0.001, 0.177), respectively. Compared with water samples from facilities without established hygiene management systems and with incomplete hygiene management information, those from facilities with hygiene management systems and complete hygiene management information had higher qualified rates, with ORs (95% CIs) of 0.086 (0.014, 0.514) and 0.098 (0.020, 0.473), respectively. Compared with water samples from facilities that had never undergone water quality testing, water samples from facilities with water quality testing conducted semi-annually or annually had higher qualified rates, with ORs (95% CIs) of 0.004 (0.001, 0.063). Water samples from cement-lined storage and supply facilities had lower qualified rates than those from stainless steel facilities, with ORs (95% CIs) of 4.533 (1.271, 16.172). Conclusion In 2024, the hygiene status of drinking water in self-built water supply facilities within a region located in southeast China was suboptimal. It is necessary to strengthen water purification, improve and implement the drinking water hygiene management system, regularly carry out water quality testing, and enhance the water quality of facilities with unqualified water samples to effectively ensure drinking water safety. Moreover, this study also provides a reference for hygiene-related emergency response in the event of sudden water pollution incidents and disaster relief tasks in the future.