Introgression of resistance genes from wild relatives offers a valuable source of genes for wheat breeders to cope with the constantly evolving rust pathogens. We characterized near-isogenic lines (NILs) of durum wheat, with and without the alien leaf rust resistance genes Lr19/Sr25 or Lr47, in four genetic backgrounds including the two Mexican cultivars Atil C2000 and Rio Colorado, the Moroccan cultivar Nassira, and the desert cultivar Kofa. Replicated field trials were conducted over several growing seasons, at three Western Canadian environments and under full irrigation and reduced irrigation in Mexico, with the aim of evaluating the agronomic and quality attributes of the NILs and checks. The presence of the Lophopyrum ponticum introgression carrying Lr19/Sr25 and the endosperm yellow pigment locus Psy-E1, resulted in significantly higher total yellow pigment content, an important target in durum wheat breeding. Lines with the Triticum speltoides segment carrying Lr47consistently showed higher grain protein concentration. Depending on the genetic background, both alien segments had either positive or neutral effect on gluten strength. However, grain yield penalties, reduced thousand kernel weights and a lower grain density were associated with both translocations, in most environments. The genomic structure of these NILs was investigated using the wheat iSelect 90K SNP array to identify molecular markers associated with donor DNA in each NIL. Physical mapping of these SNP markers to the durum wheat reference sequence (cv. Svevo) showed that the introgressed segments on chromosome 7A spanned intervals ranging from 39 Mb for lines carrying Lr19/Lr25, to 468 Mb for lines carrying Lr47. The identified markers can be used in future breeding programs to select resistant lines with small introgressions that may result in reduced effects on agronomic performance.