The physiology of stay-green and root traits in wheat were studied using crop modelling and new phenotyping techniques developed to accelerate genetic progress toward improved adaptation to water-limited environments. A modelling approach was used to evaluate potential impacts of a range of root traits in target environments revealing that increased root extractable water at depth can improve crop adaptation of wheat in all major Australian cropping regions. To study the genetics of root and stay-green traits, three nested association mapping (NAM) populations have been generated by crossing a reference parent adapted to each of Australia’s three major cropping regions with donor lines for adaptive traits, generating over 1500 recombinant inbred lines. A high throughput root trait screening technique was developed and used to characterize NAM lines. A method was also developed to objectively characterize novel stay-green traits for hundreds of genotypes in standard field trial plots. The NAM lines were phenotyped for yield and stay-green traits at multiple locations in rain-fed environments with various levels of water-limitation or under irrigation. Environmental characterization of water-stress timing and severity using simulation modelling allowed estimation of trait and QTL values in different environment types. Particular traits were associated with superior adaptation to certain environment types. Many lines with adaptive root and stay-green traits exhibited superior yield to the reference parent in relevant target environments. We believe that this combination of technologies is increasing understanding of physiological adaptation to particular environments and helping accelerate genetic progress.