Increasing access to water, sanitation and hygiene (WASH) in schools improves health and performance among learners. School WASH programs are being scaled-up globally, however little is known about how they are monitored and evaluated. We studied 21 organizations implementing WASH in school programs to assess monitoring and evaluation (M&E) policies and practices. Five barriers emerged: (1) logistical challenges; (2) limited staff capacity; (3) limited funding; (4) inadequate management systems; and (5) socio-political barriers. The findings highlight the need to better integrate M&E into government systems that will endure post-implementation. Further, there is a need to expand the data collected and improve the quality of national monitoring systems. This will likely require additional human and financial resources that can then translate into better planning and budgeting with the end goal of providing a hygienic environment for children to learn and grow.