Contaminated drinking water causes morbidity and mortality worldwide, especially in low- and middle-income countries. Drinking water quality has been studied extensively in household settings, but little research is available on drinking water quality in schools. School settings are of particular importance, because children are more susceptible than adults to a variety of diseases from contaminated drinking water. Many school water, sanitation and hygiene (WaSH) interventions have been studied for their efficacy to reduce diarrheal disease incidence, but few have evaluated drinking water quality, which reflects an important exposure pathway between WaSH services and health outcomes. Using school surveys developed from internationally established WaSH indicators and field microbiological water quality tests, we studied 374 rural schools in Mozambique and Uganda to understand the association between specific WaSH services and drinking water microbiological contamination, specifically testing most probable number (MPN) of Escherichia coli, an indicator of fecal contamination, per 100 mL. In Mozambique and Uganda, 71% and 83% respectively of rural schools had low risk drinking water quality (<1 E. coli/100 mL); thirteen percent and seven percent had very high-risk water quality (≥100 E. coli/100 mL). When accounting for all WaSH services studied, schools that used an improved-type water source had 0.22 times less E. coli in stored drinking water in Mozambique (95% CI: 0.07, 0.65) and 0.12 times less E. coli in Uganda (95% CI: 0.02, 0.80). In Mozambique, use of a water source within 30 minutes for travel and collection and the presence of water and soap/ash for handwashing were also significantly associated with less E. coli in drinking water. The findings of this study provide public health practitioners with implementable WaSH services to improve school drinking water quality, which has implications for the health, learning environment, and cognitive development of school children in rural Mozambique and Uganda.