The availability of safe water, sanitation, and hygiene (WASH) facilities in schools is essential for a healthy learning environment and achieving for sustainable development goals (SDGs) 4 and 6. Despite its importance, comprehensive studies on drinking water quality, sanitation, and hygiene in schools are scarce. This study explicitly assessed the WASH services and gaps in 43 educational institutions, located in Tongi, Bangladesh, through field and laboratory investigations. Thirteen physicochemical and bacteriological parameters were analyzed, and water quality was classified using an Integrated Water Quality Index (IWQI). Hygiene and sanitation were evaluated through observations and data from school administrators on water sources, toilets, handwashing facilities, and solid waste management. Results showed that WASH services exceeded the national average, but all schools had dangerously high Escherichia coli levels (mean: 43.95 CFU/100 mL) in drinking water, posing health risks. Additionally, 89.72% of samples showed elevated manganese levels, 35% had high iron, and 41.86% had increased conductivity. About 35% of water was unsuitable for drinking based on IWQI. Schools lacked the capacity to monitor WASH quality, especially drinking water. A strategic framework for safe WASH facilities is recommended. The findings can lead the policymakers to prioritize the improvements in WASH facilities for attaining SDG 6.