Wheat productivity is commonly limited by a lack of water essential for growth. Carbon isotope discrimination (Δ), through its negative relationship with transpiration efficiency, has been used in selection of higher wheat yields in breeding for rainfed environments. The potential also exists for selection of increased Δ for improved adaptation to irrigated and high rainfall environments. Selection efficiency of Δ would be enhanced with a better understanding of its genetic control. Three wheat mapping populations (Cranbrook/Halberd, Sunco/Tasman and CD87/Katepwa) containing between 161 and 190 F₁-derived, doubled-haploid progeny were phenotyped for Δ and agronomic traits in 3-5 well-watered environments. The range for Δ was large among progeny (c. 1.2-2.3per thousand), contributing to moderate-to-high single environment (h ² = 0.37-0.91) and line-mean (0.63-0.86) heritabilities. Transgressive segregation was large and genetic control complex with between 9 and 13 Δ quantitative trait loci (QTL) identified in each cross. The Δ QTL effects were commonly small, accounting for a modest 1-10% of the total additive genetic variance, while a number of chromosomal regions appeared in two or more populations (e.g. 1BL, 2BS, 3BS, 4AS, 4BS, 5AS, 7AS and 7BS). Some of the Δ genomic regions were associated with variation in heading date (e.g. 2DS, 4AS and 7AL) and/or plant height (e.g. 1BL, 4BS and 4DS) to confound genotypic associations between Δ and grain yield. As a group, high Δ progeny were significantly (P < 0.10-0.01) taller and flowered earlier but produced more biomass and grain yield in favorable environments. After removing the effect of height and heading date, strong genotypic correlations were observed for Δ and both yield and biomass across populations (r g = 0.29-0.57, P < 0.05) as might be expected for the favorable experimental conditions. Thus selection for Δ appears beneficial in increasing grain yield and biomass in favorable environments. However, care must be taken to avoid confounding genotypic differences in Δ with stature and development time when selecting for improved biomass and yield especially in environments experiencing terminal droughts. Polygenic control and small size of individual QTL for Δ may reduce the potential for QTL in marker-assisted selection for improved yield of wheat.