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Floods cause extensive damage in high-income countries, including the United States, but problems are more severe in low- and middle-income countries (LMICs) that lack preventative and mitigating infrastructure. Marginalized children’s education in LMICs might be particularly vulnerable. Using the Indian Human Development Survey, we investigate flood exposure implications for the education of school-age rural children, paying particular attention to children from marginalized groups. Results show that lower-caste Hindu, Muslim, and poorer children with less-educated parents in agricultural households are more likely to experience flooding. Interactions between flooding and marginalization characteristics indicate that flood exposure is associated with disproportionately negative learning outcomes for girls and that economic resources may mitigate flood exposure effects on delayed school progress. While greater exposures for marginalized groups are concerning, the limited number and modest magnitudes of documented negative effect heterogeneities for marginalized children are somewhat better news.