Background: Within the goals of the Protocol on Water and Health, Bosnia and Herzegovina has set the objective of improving Water, Sanitation, and Hygiene (WASH) in primary schools. The baseline WASH survey in primary schools is planned as the first activity in its achievement. The aim of the research is to examine the state of WASH in primary schools in the Republic of Srpska. Methods and Objectives: This survey was conducted from September 2019 to March 2020 in the Republic of Srpska. We evaluated the condition of WASH in 66 primary schools. Two primary instruments were employed for data collection: a survey questionnaire administered to school administrative staff and a checklist focusing on the hygienic and sanitary attributes of individual toilets and handwashing facilities, based on WHO and UNICEF guidelines (2019). Results: The survey results indicated that all investigated schools provided basic water services. Additionally, 75.7% of toilets and 61.2% of handwashing facilities met basic sanitary and hygiene standards. However, critical infrastructure gaps were identified, including the absence of gender-segregated toilets, insufficient toilet paper, lack of trash bins in stalls, and inadequate accessibility for the pupils with disabilities. Only 25 toilets (7.7%) were adapted for disabled pupils. Moreover, while menstrual hygiene education is essential, only 41 schools (62.1%) provided it. Conclusions: Our survey underscores that children with disabilities face significant barriers to accessing appropriate toilet facilities, and girls encounter inadequate menstrual hygiene management. Addressing these deficiencies is crucial for advancing Sustainable Development Goals, particularly Goal 10 (reducing inequality) ang Goal 4 (achieving gender equality). Effective solutions require collaboration between public health initiatives and local communities to foster a supportive and inclusive school environment that meets the diverse needs of all students.