Salinity stress tolerance in durum wheat is strongly associated with a plant’s ability to control Na+ delivery to the shoot. Two loci, termed Nax1 and Nax2, were recently identified as being critical for this process and the sodium transporters HKT1;4 and HKT1;5 were identified as the respective candidate genes. These transporters retrieve Na+ from the xylem, thus limiting the rates of Na+ transport from the root to the shoot. In this work, we show that the Nax loci also affect activity and expression levels of the SOS1-like Na+/H+ exchanger in both root cortical and stelar tissues. Net Na+ efflux measured in isolated steles from salt-treated plants, using the non-invasive ion flux measuring MIFE technique, decreased in the sequence: Tamaroi (parental line)>Nax1=Nax2>Nax1:Nax2 lines. This efflux was sensitive to amiloride (a known inhibitor of the Na+/H+ exchanger) and was mirrored by net H+ flux changes. TdSOS1 relative transcript levels were 6–10-fold lower in Nax lines compared with Tamaroi. Thus, it appears that Nax loci confer two highly complementary mechanisms, both of which contribute towards reducing the xylem Na+ content. One enhances the retrieval of Na+ back into the root stele via HKT1;4 or HKT1;5, whilst the other reduces the rate of Na+ loading into the xylem via SOS1. It is suggested that such duality plays an important adaptive role with greater versatility for responding to a changing environment and controlling Na+ delivery to the shoot.