Soil salinity, sodicity, and high extractable boron (B) are thought to reduce wheat yields on alkaline soils of south-eastern Australia; however, little quantitative information on yield penalties to edaphic constraints is available. The relationships between wheat yield of a B-tolerant cultivar and soil physicochemical conditions in the Victorian Mallee were explored using ridge regression analysis, using natural variation in the field. Wheat yields in the survey ranged from 1.3 to 6.1 Mg/ha, with low yields attributed to inadequate soil water supply during pre-anthesis growth. Crop sequences, fallow–wheat, and pulse–wheat left greatest soil water prior to sowing of the wheat crop, and lucerne–wheat the least. A descriptive model explained 54% of variation in wheat yield, with rainfall around anthesis, available soil water in the 0.10–0.40 m layer, nitrate in the 0–0.10 m layer at sowing and salinity, and sodicity in the 0.60–1.00 m layers being important factors. Subsoil salinity (ECe) and sodicity (ESP) appear to be effective surrogates for estimating the likelihood of water extraction in the deep subsoil. The analyses suggest that subsoils need to have an ECe <8 dS/m and ESP < 19% for crops to make use of water deep in the profile. Although soluble B ranged from 2 to 52 mg/kg in the 0.60–1.00 m layer of the alkaline soils considered, B appeared to have little correlation with root growth, water extraction, or yield of wheat, which has been attributed to B-tolerance of the cultivar tested and/or the overbearing effect of high Na+ in these soils.