We employed a cluster randomized trial design to measure the impact of a school based water, sanitation, and hygiene (WASH) improvement on pupil enrollment and on gender parity in enrollment, in primary schools in Nyanza Province, Kenya (2007-2009). Among schools with poor water access during the dry season, those that received a water supply, hygiene promotion and water treatment (HP&WT) and sanitation improvement, demonstrated increased enrollment (β=0.091 [0.009, 0.173] p=0.03), which translates to 26 additional pupils per school on average. The proportion of girls enrolled in school also increased by 4% (prevalence ratio (PR)=1.04 [1.00, 1.07] p=0.02). Among schools with better baseline water access during the dry season (schools that didn't receive a water source), we found no evidence of increased enrollment in schools that received a HP&WT intervention (β=0.016 [-0.039, 0.072] p=0.56) or the HP&WT and sanitation intervention (β=0.027 [-0.028, 0.082]p=0.34), and there was no evidence of improved gender parity (PR=0.99 [0.96, 1.02] p=0.59, PR=1.00 [0.97, 1.02] p=0.75, respectively). Our findings suggest that increased school enrollment and improved gender parity may be influenced by a comprehensive WASH program that includes an improved water source; schools with poor water access during the dry season may benefit most from these interventions.