BACKGROUND: Inadequate water, sanitation, and hygiene (WASH) infrastructure in rural healthcare facilities in India, poses significant challenges to effective infection control, contributing to the prevalence of healthcare-associated infections (HAIs) and poor patient outcomes. Despite ongoing global efforts to enhance WASH standards, these facilities often lack the necessary resources and management systems to sustain improvements. Supportive supervision has emerged as a potential strategy to address these gaps. This study aimed to improve the water, sanitation, and infection control practices in Rural health facilities of Jodhpur District through supportive supervision. METHODS: This study presents the findings of an intervention study conducted in Luni Block of the Jodhpur district. All the healthcare facilities (6 PHCs and 5 CHCs) in that block were included and baseline assessment was done. The intervention was provided through supportive supervision covering various domains of Water and Sanitation for Health Facility Improvement Tool (WASH FIT). After three months, a follow-up assessment was done in all the Health Care Facilities (HCFs). Endline assessment was done after three months of the follow-up assessment using the same tool. Water and swab samples from the labour room were collected from the facilities for microbiological surveillance during the baseline and endline assessments. RESULTS: During the baseline, none of the facilities included in this study had a more than 60% bed occupancy rate. Average OPD attendance in CHCs was 57, and in PHCs it was 22. None of the facilities had adequate human resources as per IPHS 2012. The significant issues in water-related practices were quality, accessibility, safe storage, periodic testing of chlorine residue, and sanitation inspection risk score. Unable to meet menstrual hygiene-related needs, improper cleaning records, and inadequate usage of PPE for waste disposal were significant gaps in sanitation-related practices. The unavailability of functional hand hygiene stations, non-adherence to hand hygiene compliance activities, and inadequate knowledge regarding the correct concentration of cleaning solution were identified as potential lacunae related to hygiene. All the facilities had shown statistically significant improvement in WASH FIT scores across all four domains post-intervention. CONCLUSIONS: Practices related to water, sanitation, hygiene, and infection control in health care facilities of rural Jodhpur were not satisfactory. There were specific gaps in all these domains. The intervention in the form of capacity building of healthcare workers, formation of an Infection Control Committee, and continuous supportive supervision was found effective.