The ion toxicities of aluminium (Al), manganese (Mn) and iron (Fe) induced in transiently waterlogged acid soils decrease root and shoot growth and grain yield more in intolerant than tolerant wheat genotypes. Whether these tolerances might also enhance grain yield in moisture-limited acid soils is not known. Wheat genotypes contrasting in ion toxicity tolerances (differing 6-fold for Al, 14-fold for Mn and 2.7-fold for Fe tolerance, quantified via relative root length (Al) or relative root dry weight (Mn and Fe)), but otherwise having a similar yield potential and maturity, were evaluated in plots with and without lime in multi-location field experiments (including two dry and one non-moisture-limiting site) in the Western Australian wheatbelt. Liming reduced surface soil acidity, and increased grain yield more in ion-toxicity tolerant than intolerant genotypes. The combined adverse effect of soil acidity and drought reduced relative grain yield less in Al- and Mn-tolerant genotypes (68%, 2347 kg ha^–1) than intolerant genotypes (76%, 2861 kg ha^–1) in drought-stressed environments. It appears that a deep root system to allow uptake of water from deep horizons in acidic soils with a dry surface layer is contingent on tolerance to multiple ion toxicities.