The progressive increase in the global population and the rapidly changing climate have put unprecedented pressure on crop production. Cowpea is one of the world’s most important leguminous crops, contributing to food security and environmental sustainability. However, cowpea productivity is limited due to waterlogging stress. The main objective of this study was to explore physiological and biochemical mechanisms to understand how cowpea genotypes respond to waterlogging stress. Four studies were conducted in controlled and field conditions to achieve these objectives. Study 1 characterized the waterlogging tolerance of 30 cowpea genotypes in a controlled environment using 24 morphophysiological parameters with waterlogging tolerance coefficients and multivariate analysis methods. 10% of the genotypes exhibited high tolerance to waterlogging stress, and the genotypes UCR 369 and EpicSelect.4 were identified as the most and least waterlogging tolerant, respectively. Study 2 evaluated the key parameters influencing carbon fixation of UCR 369 and EpicSelect.4 at the reproductive stage. The less tolerant EpicSelect.4 experienced high downregulation of stomatal and non-stomatal limiting factors during waterlogging and recovery, resulting in decreased carbon assimilation rates. UCR 369 rapidly developed adventitious roots, maintained biomass, and restored pigments and metabolites to sustain photosynthesis. A two-year field experiment was conducted in study 3 to quantify the effects of waterlogging on the yields, physiology, and biochemistry of cowpeas at different growth stages. The most apparent impact of waterlogging stress occurred at the reproductive stage, followed by the vegetative and maturity growth stages. Studies suggest that diverse cowpea genotypes have distinct physiological and biochemical mechanisms in response to waterlogging stress. In addition, the tolerant genotypes and traits identified herein can be used in genetic engineering and cowpea breeding programs that integrate increased yield with waterlogging stress tolerance.