Access to improved water supplies and sanitation generally reduces childhood diarrhea incidence. Using a cross-sectional stratified cluster sampling design, interviews were conducted among grade 4-6 primary schoolchildren from 10 primary schools in highland and lowland districts of Pursat Province, Cambodia, in both June (rainy season) and December (dry season) 2009 to determine the demographics and water sources/sanitation used. Parents also recorded any incidents of diarrhea in their children over those months. We explored the sociodemographic factors associated with use of improved water sources/sanitation, using mixed effect modelling. Participation was 84.7% (1,101/1,300). About half exclusively used improved water sources but less than 25% had access to improved sanitation during both seasons. Adjusting for clustering within households and within individuals over time, exclusive use of improved water sources and sanitation were associated with the following: dry season, more permanent housing type, family size < 8 members, and higher levels of education. Exclusive use of improved sanitation was associated with good hygiene practices and exclusive use of improved water sources was associated with male gender. Access to improved water sources and sanitation among rural Cambodian primary schoolchildren can be improved, particularly in those with lower socio-economic status. Programs to promote use of improved water sources/sanitation need to target less educated parents.