Subsoil physicochemical constraints such as primary salinity and high boron (B) can significantly reduce grain yields across wide areas of Australia. Financially viable amelioration options are limited for cropping systems on these soils, which has raised interest in ‘genetic solutions’. Increasing the tolerance of crops to high salinity and boron that typically co-exist within alkaline soils offers the potential for substantial yield benefits. To assess the contribution that genetic variation can make to crop yield, closely related genotypes differing in B and/or Na+ tolerance of bread and durum wheat, barley, and lentil were compared by growing the different lines in intact soil cores of 2 Calcarosol profiles differing in level of subsoil constraints (‘hostile’/’benign’). The hostile profile had salinity increasing to EC1 : 5 ~1.2 dS/m and B ~18 mg/kg to 0.60 m, whereas in the benign soil EC1 : 5 did not exceed ~0.6 dS/m and B ~11 mg/kg. Grain yields were significantly less on the hostile soil than the benign soil for barley (34%), bread wheat (20%), durum wheat (31%), and lentil (38%). Accumulation of B in shoots was significantly lower on the hostile soil across all crop species, indicating high sodium within the soil was associated with inhibited uptake of B in plants. In contrast, accumulation of Na+ was greater for all cereal crops in the hostile soil compared with the benign soil. Lentil plants with reputed sodium tolerance (CIPAL415) produced a significant yield benefit on both the benign and hostile soil over the commercial line, Nugget. The lentil line with combined Na+ and B tolerance (02-355L*03Hs005) also produced an additional yield increase over CIPAL415 on the hostile soil; however, yield was equivalent on the benign soil. For durum wheat, 2 genotypes differing in Na+ tolerance, containing either the Nax1 or Nax2 genes, accumulated less sodium in the straw than the parent cv. Tamaroi within the hostile soil; however, this did not translate to a yield advantage. For barley, there was no difference in either grain yield or B uptake in either the grain or straw between the B-tolerance line 03_007D_087 and its parent cv. Buloke. Similarly, there was no difference in either grain yield or B uptake between the bread wheat Schomburgk and its B-tolerant near-isogenic line BT-Schomburgk. This study suggests that of the cereal lines tested, there was no obvious benefit in lines with potentially improved tolerance for a single, specific subsoil constraint on alkaline soils where multiple potential constraints exist. In contrast, in lentils, incorporating tolerance to Na+ and B did show promise for increased adaptation to soils with subsoil constraints.