Theory and empirical evidence have demonstrated that 13C discrimination (∆) by leaves of C3 plants may be associated with intrinsic water‐use efficiency or productivity. Consequently, selection for ∆ has potential value in breeding plants with improved adaptation. This study evaluates genotypic differences in ∆ among cowpea [Vigna unguiculata (L.) Walp.] and genotype ✕ drought level interactions, and compares ∆ measured in leaves and grains. Sixty cowpea accessions were subjected to drought by growing them on stored soil moisture in six randomized blocks, and genotypes differed significantly (P < 0.001) in leaf ∆. Seventeen cowpea accessions were grown under weekly irrigation (wet) and stored moisture (dry) conditions in four randomized‐split blocks. Genotypes differed significantly in ∆ under both conditions using either leaves or grains. Plants under dry conditions had lower ∆, which theory predicted could be associated with 62% higher water‐use efficiency. The same plants showed a 62% higher ratio of CO2 assimilation rate to leaf diffusive conductance. Genotypic rankings for ∆ were similar under wet and dry conditions for most genotypes, but a significant (P < 0.05) genotype ✕ drought interaction was observed, which was mainly due to one genotype. Correlations between ∆ in grain and subtending leaves were highly significant (P < 0.001), but two genotypes exhibited substantial differences in ranking for ∆ determined in grain compared with leaves. Genotypic differences were more readily detected in leaves than grains with broad sense heritabilities of 0.76 and 0.35, respectively. Heritabilities were similar under wet and dry conditions.