Low-pH stress and Al<sup>3+</sup> toxicity affect root growth in acid soils. It was hypothesized that the capacity of genotypes to maintain Mg<sup>2+</sup> uptake in acidic environments may contribute to low-pH and Al resistance, but explicit evidence is lacking. In this work, an Al-resistant <i>alr104</i> mutant and two Al-sensitive mutants (<i>als5</i> and <i>als3</i>) of <i>Arabidopsis thaliana</i> were compared with the wild type (Col-0) for Mg<sup>2+</sup> uptake and intracellular Mg<sup>2+</sup> concentration under low-pH and combined low-pH/Al stresses. Magnesium accumulation in roots was measured in long-term (7 d) experiments. The Mg<sup>2+</sup> fluxes were measured using ion-sensitive microelectrodes at the distal elongation and the mature root zones in short-term (0–60 min) experiments. Intracellular Mg<sup>2+</sup> concentrations were measured in intact root cells at the distal elongation zone using magnesium-specific fluorescent dye and fluorescent lifetime imaging (FLIM) analysis. Under low-pH stress, Arabidopsis mutants <i>als5</i> and <i>alr104</i> maintained a higher Mg concentration in roots, and had greater Mg<sup>2+</sup> influx than the wild type and the <i>als3</i> mutant. Under combined low-pH/Al treatment, Al-resistant genotypes (wild type and <i>alr104</i>) maintained a higher Mg<sup>2+</sup> accumulation, and had a higher Mg<sup>2+</sup> influx and higher intracellular Mg<sup>2+</sup> concentration than Al-sensitive genotypes (<i>als3</i> and <i>als5</i>). Overall, these results show that increased Mg2+ uptake correlates with an enhanced capacity of Arabidopsis genotypes to cope with low-pH and combined low-pH/Al stresses.