Genotypic variation in crop response to drought depends on agronomic, environmental and genetic factors, and only limited work has compared responses of crop species to water limitation. Twenty genotypes of peanut (Arachis hypogaea L.) and of cowpea (Vigna unguiculata (L.) Walp) were tested in lysimeters under well-watered (WW) and water-stress (WS) conditions during two seasons, a post-rainy season with high evapotranspiration and a rainy season with low evapotranspiration (ET), in order to assess: (i) variability in the agronomic response to stress within and between species across the seasons; (ii) the water requirement of the two crops in each season; and (iii) the stress effect on harvest index (HI), transpiration efficiency (TE), pod yield and haulm yield. Cowpea required less water than peanut during the two seasons, and water use in cowpea varied less across seasons than in peanut. Peanut yield was more sensitive to water stress than cowpea yield, although its water use under WS was higher than in cowpea. Also, under WS conditions, TE, HI and pod yield were more stable across season in cowpea than in peanut. In the post-rainy season, the decrease in pod yield and HI under WS was higher in peanut (95% and 80%, respectively) than in cowpea (70% and 35%). In addition, TE was less affected by WS in cowpea (5%) than in peanut (24%). HI explained a large part of yield variation in both crops, especially under WS. Under WW, water use explained a large portion of the residual yield variations unexplained by HI, although TE also explained a substantial part of the variation in cowpea. Under WS, the main determinant of residual yield variations in both crops was TE. Generally, genetic variation for water use, TE and HI was found in both species across water regimes and seasons. A notable exception was the absence of variation in peanut water use and TE in the rainy season. Our results showed that cowpea, with lower water requirement and efficient water use under a high-ET season, was more resilient to water-limited and high-ET conditions than peanut.