The progress in plant breeding for salinity stress tolerance is handicapped by the lack of understanding of the specificity of salt stress signalling and adaptation at the cellular and tissue levels. In this study, we used electrophysiological, fluorescence imaging and real-time qPCR tools to elucidate the essentiality of the cytosolic Na+ extrusion in functionally different root zones (elongation; meristem; mature) in a large number of bread and durum wheat accessions. We show that the difference in the root’s ability for vacuolar Na+ sequestration in the mature zone may explain differential salinity stress tolerance between salt sensitive durum and salt tolerant bread wheat species. Bread wheat genotypes also had on average 30% higher capacity for net Na+ efflux from the root elongation zone, providing the first direct evidence for the essentiality of root salt exclusion trait at the cellular level. At the same time, cytosolic Na+ accumulation in the root meristem was significantly higher in bread wheat, leading to suggestion that this tissue may harbor a putative salt sensor. This hypothesis was then tested by investigating patterns of Na+ distribution and relative expression level of several key genes related to Na+ transport in leaves in plants with intact roots and those in which the roots meristem were removed. We show that tampering with this sensing mechanism has resulted in a salt-sensitive phenotype, largely due to compromised plant’s ability to sequester Na+ in mesophyll cell vacuoles. The implications of these findings for plant breeding for salinity stress tolerance are discussed.