Across sub-Saharan Africa, delayed care-seeking is a driver of severe malaria. Climate change is intensifying the frequency and severity of rainfall events, often resulting in flooding which can disrupt access to healthcare. Yet the effects of flooding on hospitalizations attributable to malaria has not been examined.

This study is a secondary analysis of cross-sectional data collected during a cluster randomized trial in rural western Uganda (NCT06870344). All households in selected villages along three flood-prone rivers were eligible. Surveys documenting household characteristics, resident demographics, exposure to flooding, and child health history were administered. Analyses were conducted using a mixed-effects logistic regression with random effects for household assessing indirect flooding exposure, defined as no flooding of the household or property but reported disruptions in daily life including work, school, and access to healthcare and markets, and direct flooding exposure, defines as flooding of the household or property.

The analysis included 10,948 children from 3,754 households. Indirect flooding exposure increased the odds of pediatric malaria hospitalization by 1.75 times (95% CI: 1.06–2.90), while direct exposure increased the odds by 2.45 times (95% CI: 1.54–3.91), compared with no exposure. Among exposed households, work disruptions were associated with nearly fourfold higher odds of hospitalization (OR = 3.94; 95% CI: 2.17–7.14), and disruptions in care-seeking with nearly twofold higher odds (OR = 1.89; 95% CI: 1.01–3.40). No association was found between the number of flooding events and hospitalization.

These findings suggest that indirect consequences of flooding, particularly financial and livelihood disruptions, may delay care-seeking and increase malaria hospitalization risk. Interventions addressing post-flood economic and access barriers could reduce severe malaria outcomes in flood-prone regions.