Grain yield and the natural abundance of the stable isotope compositions of carbon (δ13C), oxygen (δ18O) and nitrogen (δ15N) of mature kernels were measured during 3 consecutive years in 10 durum wheat genotypes (five landraces and five modern cultivars) subjected to different water and N availabilities in a Mediterranean location and encompassing a total of 12 trials. Water limitation was the main environmental factor affecting yield, δ13C and δ18O, whereas N fertilisation had a major effect on δ15N. The genotypic effect was significant for yield, yield components, δ13C, δ18O and δ15N. Landraces exhibited a higher δ13C and δ15N than cultivars. Phenotypic correlations of δ13C and δ18O with grain yield were negative, suggesting that genotypes able to sustain a higher water use and stomatal conductance were the most productive and best adapted; δ15N was also negatively correlated with grain yield regardless of the growing conditions. δ13C was the best isotopic trait in terms of genetic correlation with yield and heritability, whereas δ18O was the worst of the three isotopic abundances. The physiological basis for the different performance of the three isotopes explaining the genotypic variability in yield is discussed.