Waterlogging is an important environmental stress limiting the productivity of crops worldwide. Cowpea ( Vigna unguiculata L) is particularly sensitive to waterlogging stress during the reproductive stage, with a consequent decline in pod formation and yield. However, little is known about the critical processes underlying cowpea’s responses to waterlogging during the reproductive stage. Thus, we investigated the key parameters influencing carbon fixation, including stomatal conductance (g _s), intercellular CO ₂ concentration, chlorophyll content, and chlorophyll fluorescence, of two cowpea genotypes with contrasting waterlogging tolerance. These closely related genotypes have starkly contrasting responses to waterlogging during and after 7-days of waterlogging stress (DOW). In the intolerant genotype (‘EpicSelect.4’), waterlogging resulted in a gradual loss of pigment and decreased photosynthetic capacity as a consequent decline in shoot biomass. On the other hand, the waterlogging-tolerant genotype (UCR 369) maintained CO ₂ assimilation rate ( A), stomatal conductance (g _s), biomass, and chlorophyll content until 5 DOW. Moreover, there was a highly specific downregulation of the mesophyll conductance (g _m), maximum rate of Rubisco (V _cmax), and photosynthetic electron transport rate (J _max) as non-stomatal limiting factors decreasing A in EpicSelect.4. Exposure of EpicSelect.4 to 2 DOW resulted in the loss of PSII photochemistry by downregulating the PSII quantum yield (F _v/F _m), photochemical efficiency (Ф _PSII), and photochemical quenching (qP). In contrast, we found no substantial change in the photosynthesis and chlorophyll fluorescence of ‘UCR 369’ in the first 5 DOW. Rather, UCR 369 rapidly developed adventitious roots (ARs), maintained biomass accumulation, and elongated stems, enabling the genotypeto maintain nutrient absorption and photosynthesis during the early period of waterlogging. However, compared to the control, both cowpea genotypes could not fully recover their photosynthetic capacity after 7 DOW, with a larger decline in EpicSelect.4. Overall, our findings suggest that rapid AR formation and stem elongation appear to play critical roles in cowpea’s waterlogging tolerance, with the waterlogging-tolerant genotype also maintaining considerable carbon fixation during the reproductive stage.