Water born diseases are a constant challenge to the population health among the secondary school students in Nigeria and especially in the rural regions with lack of water and sanitation facilities. This research investigated how the education of senior secondary students in Oyo East Local Government Area, Oyo State in Biology and other Health Science subjects affects hygiene practices and the prevention of waterborne diseases among students in the subject areas. Based on the Health Belief Model and Neo-Functionalist theory, the study sample was a descriptive survey of 510 students who were selected based on a multistage sampling technique in three randomly selected public secondary schools. Data were gathered through a validated researcher-created questionnaire (Cronbach 0.83) and analyzed using descriptive statistics, multiple linear regression and one-way ANOVA with a significance level of 0.05. Results showed that there was high level of hygiene practices among students (Grand Mean = 2.92), showing that Biology and Health Science instruction has a positive influence on health behavior. The multiple linear regression revealed statistically significant relationship between education quality, hygiene practices, and prevalence of waterborne diseases [F (2, 507) = 3.66, p = 0.027], with the education quality being a statistically significant independent predictor of lower disease rates (= -0.116, p = 0.009). Nevertheless, one-way ANOVA did not find a significant difference in academic absenteeism between disease burden levels [F (2, 507) = 0.008, p = 0.992], which suggested a uniform perceived academic impact across disease burden levels. The report finds that enhancement of science education quality is a feasible option of lessening the burden of waterborne diseases. It suggests the incorporation of realistic WASH literacy into the curriculum and the remediation of the infrastructural gaps in the school water and sanitation infrastructure.