Subsoil physicochemical constraints can limit crop production on alkaline soils of south-eastern Australia. Fifteen farmer paddocks sown to a range of crops including canola, lentil, wheat, and barley in the Wimmera and Mallee of Victoria and the mid-north and Eyre Peninsula of South Australia were monitored from 2003 to 2006 to define the relationship between key abiotic/edaphic factors and crop growth. The soils were a combination of Calcarosol and Vertosol profiles, most of which had saline and sodic subsoils. There were significant correlations between ECe and Cl– (r = 0.90), ESP and B (r = 0.82), ESP and ECe (r = 0.79), and ESP and Cl– (r = 0.73). The seasons monitored had dry pre-cropping conditions and large variations in spring rainfall in the period around flowering. At sowing, the available soil water to a depth of 1.2 m (θa) averaged 3 mm for paddocks sown to lentils, 28 mm for barley, 44 mm for wheat, and 92 mm for canola. Subsoil constraints affected canola and lentil crops but not wheat or barley. For lentil crops, yield variation was largely explained by growing season rainfall (GSR) and θa in the shallow subsoil (0.10–0.60 m). Salinity in this soil layer affected lentil crops through reduced water extraction and decreased yields where ECe exceeded 2.2 dS/m. For canola crops, GSR and θa in the shallow (0.10–0.60 m) and deep (0.60–1.20 m) layers were important factors explaining yield variation. Sodicity (measured as ESP) in the deep subsoil (0.80–1.00 m) reduced canola growth where ESP exceeded 16%, corresponding to a 500 kg/ha yield penalty. For cereal crops, rainfall in the month around anthesis was the most important factor explaining grain yield, due to the large variation in rainfall during October combined with the determinant nature of these crops. For wheat, θa in the shallow subsoil (0.10–0.60 m) at sowing was also an important factor explaining yield variation. Subsoil constraints had no impact on cereal yield in this study, which is attributed to the lack of available soil water at depth, and the crops’ tolerance of the physicochemical conditions encountered in the shallow subsoil, where plant-available water was more likely to occur. Continuing dry seasonal conditions may mean that the opportunity to recharge soil water in the deeper subsoil, under continuous cropping systems, is increasingly remote. Constraints in the deep subsoil are therefore likely to have reduced impact on cereals under these conditions, and it is the management of water supply, from GSR and accrued soil water, in the shallow subsoil that will be increasingly critical in determining crop yields in the future.