To characterise the effect of exotic alleles introgressed in a selected set of barley Recombinant Chromosomes Substitution Lines (RCSLs), we evaluated their response to contrasting water regimes in semi-controlled field trials. We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis allowed an effective genetic dissection of morphological, developmental and agronomic traits measured. The combined approach identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. The combination of our approach with new genetic tools available for barley to identify candidate genes for difficult traits is discussed.