Productivity of grain crops grown under dryland conditions in north-eastern Australia depends on efficient use of rainfall and available soil moisture accumulated in the period preceding sowing. However, adverse subsoil conditions including high salinity, sodicity, nutrient imbalances, acidity, alkalinity, and high concentrations of chloride (Cl) and sodium (Na) in many soils of the region restrict ability of crop roots to access this stored water and nutrients. Planning for sustainable cropping systems requires identification of the most limiting constraint and understanding its interaction with other biophysical factors. We found that the primary effect of complex and variable combinations of subsoil constraints was to increase the crop lower limit (CLL), thereby reducing plant available water. Among chemical subsoil constraints, subsoil Cl concentration was a more effective indicator of reduced water extraction and reduced grain yields than either salinity or sodicity (ESP). Yield penalty due to high subsoil Cl was seasonally variable, with more in-crop rainfall (ICR) resulting in less negative impact. A conceptual model to determine realistic yield potential in the presence of subsoil Cl was developed from a significant positive linear relationship between CLL and subsoil Cl: Since grid sampling of soil to identify distribution of subsoil Cl, both spatially across landscape and within soil profile, is time-consuming and expensive, we found that electromagnetic induction, coupled with yield mapping and remote sensing of vegetation offers potential to rapidly identify possible subsoil Cl at paddock or farm scale. Plant species and cultivars were evaluated for their adaptations to subsoil Cl. Among winter crops, barley and triticale, followed by bread wheat, were more tolerant of high subsoil Cl concentrations than durum wheat. Chickpea and field pea showed a large decrease in yield with increasing subsoil Cl concentrations and were most sensitive of the crops tested. Cultivars of different winter crops showed minor differences in sensitivity to increasing subsoil Cl concentrations. Water extraction potential of oilseed crops was less affected than cereals with increasing levels of subsoil Cl concentrations. Among summer crops, water extraction potential of millet, mungbean, and sesame appears to be more sensitive to subsoil Cl than that of sorghum and maize; however, the differences were significant only to 0.7 m. Among pasture legumes, lucerne was more tolerant to high subsoil Cl concentrations than the others studied. Surface applied gypsum significantly improved wheat grain yield on soils with ESP >6 in surface soil (0–0.10 m). Subsurface applied gypsum at 0.20–0.30 m depth did not affect grain yield in the first year of application; however, there was a significant increase in grain yield in following years. Better subsoil P and Zn partially alleviated negative impact of high subsoil Cl. Potential savings from improved N fertilisation decisions for paddocks with high subsoil Cl are estimated at ~$AU10 million per annum.