Diarrhea, soil-transmitted helminth (STH) infection, and malnutrition threaten the lives of millions of children globally but particularly in the Global South, where inadequate water, sanitation, and hygiene (WaSH) drive disease risk. The aim of our study was to identify environmental and behavioral risk factors of these diseases among schoolchildren in Metro Manila, Philippines. We analyzed data from a multistage cluster sample of grade 5-10 students to investigate WaSH facilities and hygiene practices. Outcomes were self-reported diarrhea and STH infection and observed malnutrition (stunting, undernutrition, over-nutrition); we used logistic regression models to explore correlates. We included 1,558 students from 15 schools in 3 cities. Over 14% (212) of students experienced diarrhea only, 29.7% (438) experienced STH infection only, and 14% (207) experienced both diarrhea and STH infection. Over 15% (227) of students were stunted, ∼6% (87) were undernourished, and 21% (306) were over-nourished. While diarrhea was associated with poor handwashing, avoiding school restrooms, and lack of a restroom cleaning policy, STH infection was associated with students’ dissatisfaction with school restrooms. Risk of having both diarrhea and STH infection increased when school restrooms lacked water or were unclean. Being only stunted was associated with diarrhea, while being both stunted and undernourished was associated with STH infection. These findings demonstrate that adequate water supply and cleanliness of school WaSH facilities must be achieved and maintained to prevent disease. Future school-based WaSH interventions are recommended to provide clean WaSH facilities that have water, promote handwashing, and discourage avoidance of school toilets.