Climate variability and extreme weather events pose growing public health risks, especially in geographically vulnerable regions. Kerala, a southern Indian state with an extensive coastline and dense river network, is increasingly affected by sea-level rise, heavy rainfall, and recurrent floods. Children in these flood-prone areas face heightened risks of adverse health outcomes, including undernutrition. However, limited studies have examined the link between flooding and child nutrition in this region. This study assessed the nutritional status of children aged 12–59 months in Alappuzha, one of the most flood-affected districts in Kerala.

A cross-sectional survey was conducted in five flood-prone panchayats in Alappuzha using a multi-stage sampling approach. Data collected included socio-demographics, flood-related exposures, and anthropometric measurements. WHO Anthro Survey Analyzer was used to calculate Z-scores for stunting, wasting, and underweight.

The study found a high prevalence of undernutrition, with 28.25 % of children underweight, 31 % stunted, and 21 % wasted—figures exceeding recent state averages. Odds of undernutrition were higher among girls, children of less-educated mothers, and those whose fathers held elementary occupations. Children from families which were displaced to relief camps during floods had significantly higher odds of being underweight (AOR 8.43; 95 % CI: 3.87–21.3; p < 0.001) and experiencing anthropometric failure (AOR 1.84; 95 % CI: 1.13–3.04; p = 0.023).

Undernutrition among children in flood-prone areas of Kerala is elevated and linked to both socio-demographic and disaster-related factors. Findings underscore the need for longitudinal studies and targeted interventions in climate-vulnerable regions .