This study investigated the effects of waterlogging on two maize genotypes (BML6 and BML7) at two distinct seedling stages as Set 1 and Set 2 (11 – 17 days and 21 – 27 days). Waterlogging significantly impacted plant growth, leading to reduced leaf area (LA) in both genotypes. The tolerant genotype BML7 maintained a significantly larger LA (113 cm²) compared to the sensitive genotype BML6 (92.09 cm²) by the 27th day of stress exposure. Across both developmental stages, leaf senescence was more pronounced in BML6, with a 50 % leaf death rate, compared to 37 % in BML7. Waterlogging stress adversely affected plant growth, resulting in a reduction in final biomass by 20 % in BML6 and 15 % in BML7. Additionally, waterlogging led to a significant decline in relative water content (RWC) (by approximately 15 %) and chlorophyll content (by 20 %) in both genotypes. Biochemical assessments indicated marked changes, with total carbohydrate content decreasing by 15 % in BML6 and 10 % in BML7. Hydrogen peroxide (H2O2) levels increased threefold at the late seedling stage, while peroxidase (POD) activity increased by 30 % in BML7 under waterlogged conditions, suggesting a stronger antioxidant response in the tolerant genotype. These findings demonstrate significant genotypic variation in waterlogging tolerance among maize cultivars. Further research is crucial to identify key physiological, biochemical and morphological traits associated with waterlogging stress tolerance in maize. Characterizing these traits will facilitate the development of maize cultivars with enhanced resilience to waterlogging stress, a critical adaptation in light of the increasing frequency and intensity of flooding events driven by climate change.