In the Birchip region of Victorian southern Mallee, Australia (35.98°S and 142.92°E), subsoil constraints are considered to be the most important factors determining crop growth and yield. Salinity, alkalinity, and boron toxicity occur in many soils in this region and present crop simulation models have shown to perform poorly in this region, particularly due to their inability to account for multiple subsoil constraints and their interactions with the seasonal conditions. The objective of this work was to study the impact of subsoil constraints on crop physiological parameters, growth and yield of a wheat crop to help develop algorithms that could be used to improve the performance of existing crop simulation models. From a calibrated electromagnetic survey (EM 38) over an area 7m wide by 100m long, we identified three points of low, medium and high salinity levels. At these points lab tested levels of soil salinity averaged for the depth 0-0.7m were 0.25, 1.14 and 1.63 dS/m, respectively. During the cropping season crop samples were taken around each selected point, and accumulated canopy interception, radiation use efficiency, dry weight and growth rate of different organs, were calculated and leaf area, biomass and yield were measured. Soil water content at different stages of crop growth was also recorded using a neutron probe moisture meter, and the effect of salinity on plant water uptake was determined. Above ground dry weight, canopy light interception, radiation use efficiency, plant water uptake and grain yield, were all reduced by increasing salinity levels. Relative to the low salinity site, medium and high salinity levels reduced the above ground dry weight of the crop at harvest by 39.8% and 41%, accumulated intercepted radiation by 23% and 37% and radiation use efficiency by 25% and 52%, respectively. The final grain yield was 4.53, 2.69 and 2.36 t/ha, at the low, medium and high salinity sites. Crop harvest index was reduced by 1.2% and 11.7% and grain yield by 41% and 48% at medium and high salinity levels, respectively, in comparison with low salinity level. These results indicate that to account for the impact of salinity on crop yield in crop simulation models, the impacts of salinity on water use by crop, the amount of intercepted radiation, the conversion efficiency of intercepted radiation into biomass, and harvest index need to be taken into account. However, in the Birchip region of Victorian southern Mallee, where dryland farming is practiced and rain is the only source of water available to the crop, yield is limited by water availability and through this study, the simulation model will be modified to take the effect of salinity on crop water use to explain variation in grain yield at paddock level.