Drought is the single most important factor limiting soya bean (Glycine max L. Merr.) yields in the field. The following study was therefore undertaken to identify phenotypic markers for enhanced drought tolerance in nodulated soya beans. Leaf and nodule parameters were compared in three genotypes: Prima 2000, glyphosate-resistant A5409RG and Jackson, which had similar shoot biomass and photosynthesis rates at the third trifoliate leaf stage under water-replete conditions. When water was withheld at the third trifoliate leaf stage, photosynthesis, nodule numbers, nodule biomass and symbiotic nitrogen fixation (SNF) were greatly decreased. Significant cultivar–drought interactions were observed with respect to photosynthesis, which also showed a strong positive correlation with nodule SNF, particularly under drought conditions. Prima leaves had high water-use efficiencies, and they also maintained high photosynthetic electron transport efficiencies under long-term drought. Moreover, Prima had the highest shoot biomass under both water-replete and drought conditions. A-5409RG was the most drought-sensitive genotype showing early closure of stomata and rapid inhibition of photosynthesis in response to drought. In addition to classifying the genotypes in relation to drought tolerance, the results demonstrate that the ability to sustain shoot biomass under nitrogen limitation is an important parameter, which can be easily applied in germplasm screening for drought tolerance in soya bean.