Low-pH stress and Al3+ toxicity affect root growth in acid soils. It was hypothesized that the capacity of genotypes to maintain Mg2+ uptake in acidic environments may contribute to low-pH and Al resistance, but explicit evidence is lacking. In this work, an Al-resistant alr104 mutant and two Al-sensitive mutants (als5 and als3) of Arabidopsis thaliana were compared with the wild type (Col-0) for Mg2+ uptake and intracellular Mg2+ concentration under low-pH and combined low-pH/Al stresses. Magnesium accumulation in roots was measured in long-term (7 d) experiments. The Mg2+ fluxes were measured using ion-sensitive microelectrodes at the distal elongation and the mature root zones in short-term (0–60 min) experiments. Intracellular Mg2+ 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 als5 and alr104 maintained a higher Mg concentration in roots, and had greater Mg2+ influx than the wild type and the als3 mutant. Under combined low-pH/Al treatment, Al-resistant genotypes (wild type and alr104) maintained a higher Mg2+ accumulation, and had a higher Mg2+ influx and higher intracellular Mg2+ concentration than Al-sensitive genotypes (als3 and als5). 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.