Access to basic water, sanitation and hygiene services is the most effective mechanism to reduce many infectious diseases. WASH in schools related to better educational outcomes although adequate water, sanitation, and hygiene services were unavailable to millions of school-age children in Ethiopia. Therefore, it is crucial to assess the level of WASH coverage and identify factors affecting access to basic water, sanitation, and hygiene services. A cross-sectional study was carried out among 82 school facilities. A structured questionnaire and an observational checklist were used to gather the data. Water samples were taken from the schools' water storage. Descriptive and multivariable logistic regression analyses were used to analyze the data. In this study, 74.7%, 61. 3% and 37.3% of the schools had access to basic drinking water, sanitation, and hygiene services, respectively. Additionally, 21.3%, 29.4%, and 30.7% of the schools had access to limited drinking water, sanitation, and hygiene services, respectively. However, 4%, 9.3%, and 32% of the schools lacked water, sanitation, and hygiene services, respectively. We discovered that schools with male heads were 7% less likely to have access to basic hygiene services (AOR = 0.07 with 95% CI 0.01–0.5) than those with female directors. In addition, schools with hygiene and environmental health clubs had an 11.8-fold higher access rate to basic hygiene services (AOR = 11.8 with 95% CI 1.35–104) than schools without such clubs. Besides, schools that conduct WASH lessons at least once a week were 8.63 times more likely to use basic hygiene services (AOR = 8.63; 95% CI 1.18–63.22) than schools that did not. This study offers scientific evidence that could be used for sound decisions to fill the school WASH gaps. This is a unique study in determining the level of WASH coverage and identifying factors affecting access to basic hygiene services. The investigation provides some insights into how access to WASH services can be improved at the grassroots level. Federal and regional governments should implement effective interventions that assist schools to attain Sustainable Development Goal 6 by 2030. School administrators and other partner organizations should take proactive measures to enhance and maintain the WASH services.