Soybean [Glycine max (L.) Merr.] yield, when regressed on water needed to replenish 0 to 100% seasonal evapotranspiration (ET), generates an estimate of season‐specific water‐use efficiency (WUE). The impact of unpredictable water deficits might be lessened if high‐yielding genotypes had a smaller beta. Our objective was to determine the genetic basis of beta and carbon isotope discrimination (CID), a theorized indicator of transpiration efficiency (TE). A ‘Minsoy’ × ‘Noir 1’ population of 236 recombinant inbred lines (RILs), genotyped at 665 loci, was evaluated in six water treatments (100, 80, 60, 40, 20, and 0% ET) for 2 yr. Water stress was mild in 1994, but high temperatures and no rainfall in 1995 led to a drought so severe that the 100% ET treatment required 41 cm of irrigation. The 1995 yield‐to‐water regression was highly linear (28 kg ha−1 cm−1). Genotype × water (G × W) interaction was due to genotypic heterogeneity in beta The CID vs. beta correlation was low (r = 0.26), so selection for better leaf TE may not improve crop WUE. Selection of low beta (less sensitivity to drought) will be difficult, given the yield beta vs. yield correlation (r = 0.71). The major quantitative trait loci (QTL) for yield beta, yield, and CID were coincident with maturity and/or determinancy QTLs, except for a CID QTL in linkage group U09‐C2, but it had no effect on beta Genetic improvement of soybean yield performance under drought would be better achieved by coupling a high‐yield grand mean with a high‐ (not low‐) yield beta