Maize (Zea mays L.) is one of the most important cereal crops cultivated around the world. Waterlogging stress is a major production constraint of maize production in rain-fed agricultural systems. The main objective of this experiment was to investigate the effect of continuous waterlogging on morphological and biochemical traits of maize genotypes at the vegetative stage. Ten maize genotypes were treated under no waterlogging (control) and continuous waterlogging of five centimeters depth for 10 days. The treatments were applied to the plants at their 45 days of age. Visual leaf injury scores from Leaf 4 (youngest leaf is the reference point) to Leaf 7 separated tolerant and susceptible genotypes. Waterlogging stress significantly reduced the total number of live leaves and chlorophyll content in leaf tissues in susceptible genotypes. The anatomical study revealed that tolerant maize genotypes produce a large number of aerenchyma cells under waterlogging stress compared to susceptible genotypes. The enzymatic activities of ascorbate peroxidase (APX) and peroxidase (POD) exhibited a greater increase in tolerant genotypes than susceptible genotypes whereas the contents of reactive oxygen species (H2O2) greatly increased in susceptible genotypes than tolerant genotypes under waterlogging stress compared to control. Principal component 2 (PC2) indicated that increasing plant height in the genotypes BHM-14, BHM-13 and BHM-9 was associated with waterlogging tolerance. The findings of this experiment will add value to maize breeding to screen out maize genotypes for waterlogging stress tolerance.