Water, sanitation, and hygiene (WASH) services are essential for learner health and equitable education. Persistent gaps in WASH infrastructure and hygiene provision, particularly those affecting girls, remain a major challenge in low- and middle-income countries. We assessed WASH interventions, learner knowledge and perceptions, and implementation challenges and opportunities in primary schools in eThekwini District, South Africa. We conducted a cross-sectional study among Grade 7 learners using a structured questionnaire adapted from the WHO Surveillance of WASH in Schools Tool, complemented by observational checklists. Stratified random sampling yielded 129 participants (76 girls, 53 boys); 72% response rate. Quantitative data were analysed using Chi-square, Fisher’s exact, and Kruskal–Wallis tests as appropriate. Although drinking water access was generally reliable, significant gaps were observed in sanitation privacy, soap and toilet paper availability, cleanliness, and menstrual hygiene facilities. Female learners consistently reported poorer conditions than males (p < 0.05). The Hygiene Access Index differed significantly across gender and age groups (p < 0.05), reflecting inequitable provision of hygiene materials. Despite educational initiatives, substantial shortcomings persist in school WASH infrastructure and hygiene provision, disproportionately affecting girls’ dignity, well-being, and school participation. Sustaining gender-responsive WASH systems is essential for improving learner health and promoting equitable educational environments.