Subsurface soil acidity reduces the growth of roots, which can potentially decrease crop yields. However, the magnitude of these yield reductions is dependent on interactions between factors such as the depth and severity of subsurface soil acidity, plant resistance to acidity, and water and nutrient availability. The Agricultural Production Systems Simulator (APSIM) was used to examine effects of these factors and their interactions on wheat yields in the Mediterranean climatic regions of Western Australia. The model was linked to historical meteorological data of the region ( up to 90 different seasons), and was run for three locations representing low, medium and high rainfall zones and three constant but contrasting soil acidity profiles in a deep sandy soil with two wheat cultivars differing in aluminium (Al) resistance. The simulated results showed inherently high variability between seasons in grain yield, rooting depth and nitrogen leaching. Subsurface soil acidity could decrease average grain yields by up to 60%, particularly in soil profiles with acidity in deep layers. The adverse effects of acidity on wheat yields were greater in the high than the low rainfall zone. Amelioration of acidity by 75% in the entire profile or in the top 20-cm layer improved the yield of the Al-sensitive wheat cultivar. Growing Al-resistant wheat partially eliminated the negative effects of acidity on yields in soils with severe subsurface acidity and almost fully eliminated these negative effects in soils with moderate subsurface acidity. The yield benefits arising from growing Al-resistant wheat were greater than those from ameliorating acidity in the 0 - 20 cm layer by liming. Increasing nitrogen input increased yields of both Al-sensitive and Al-resistant wheat grown in acid soils in all the rainfall zones, but the yield increments were much greater in the high than the low rainfall zones. Applications of nitrogen fertilisers mitigate the effect of acidity on yields of Al-sensitive wheat in soils with shallow ( 10 - 40 cm) subsurface acidity. Furthermore, the improved yield by growing Al-resistant wheat and amelioration of acidity was correlated with increased rooting depth and was associated with decreased nitrogen leaching. Possible agronomic management options to combat the subsurface acidity problem are discussed.