Comprehensive strategies in water, sanitation, and appropriate hygiene behaviors can improve school enrolment and improve gender parity disparities. Lack of safe drinking water negatively impacts the social capital of people, especially school-going children in rural areas. In this study, we systematically evaluated and documented evidence on the barriers and facilitators in the access and adoption of safe water practices in rural schools in Laikipia County, Kenya. An ethnographic formative, collaborative implementation research design was used in an iterative and participatory process to evaluate community, socio-economic, and health system-related factors affecting water, hygiene, and sanitation strategies. Qualitative data was collected using key informant interviews (n=5) and focus groups (n=3) from various multisectoral participants. Directed content analysis was used to develop codes, categories, and themes from textual data. Data was organized according to the Promoting Action on Research Implementation in Health Services framework. The findings were classified and described under three key elements: context, evidence, and facilitation. Contextual elements showed an association of diarrhea outbreaks with unsafe hygiene practices compounded by water scarcity. The evidence elements were indicative of the applicability of water backpacks in strengthening handwashing, storage, and transport of water. Facilitation elements indicated evidence of gaps in synergy between the school health and public health systems, necessitating multisectoral collaboration and social capital capacity building. The national and county governments play an imperative role in ensuring access and continuous supply of safe drinking water in schools. This is fundamental in efforts towards reducing social inequalities of health among school-going children and building their social capital. Participatory, collaborative, multisectoral interventions and decision-making are crucial, leveraging on creating local ownership, in meeting the water consumption needs of children and communities in water-scarce regions.