Grain yield and the natural abundance of the stable isotope compositions of carbon (d13C), oxygen (d18O) and nitrogen (d15N) 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, d13C and d18O, whereas N fertilisation had a major effect on d15N. The genotypic effect was significant for yield, yield components, d13C, d18O and d15N. Landraces exhibited a higher d13C and d15N than cultivars. Phenotypic correlations of d13C and d18O 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; d15N was also negatively correlated with grain yield regardless of the growing conditions. d13C was the best isotopic trait in terms of genetic correlation with yield and heritability, whereas d18O 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.