This study compared the performance of the stable isotope composition of carbon (13C), oxygen (18O) and nitrogen (15N) by tracking plant response and genotypic variability of durum wheat to different salinity conditions. To that end, 13C, 18O and 15N were analysed in dry matter (dm) and the water-soluble fraction (wsf) of leaves from plants exposed to salinity, either soon after plant emergence or at anthesis. The 13C and 18O of the wsf recorded the recent growing conditions, including changes in evaporative conditions. Regardless of the plant part (dm or wsf), 13C and 18O increased and 15N decreased in response to stress. When the stress conditions were established just after emergence, 15N and 13C correlated positively with genotypic differences in biomass, whereas 18O correlated negatively in the most severe treatment. When the stress conditions were imposed at anthesis, relationships between the three isotope signatures and biomass were only significant and positive within the most severe treatments. The results show that nitrogen metabolism, together with stomatal limitation, is involved in the genotypic response to salinity, with the relative importance of each factor depending on the severity and duration of the stress as well as the phenological stage that the stress occurs.