It is well established that Mn toxicity to crops may occur in acid soils and under waterlogging, but there is little information on toxic thresholds in soils. This study was set-up to derive toxic thresholds for plant growth in soils and to relate toxicity of Mn to the Mn speciation in soils. Toxicity of Mn to barley (Hordeum vulgare L.) was assessed for three soils (pH 4.7–6.7) freshly amended with Mn(II) salt using root elongation and plant growth tests. A 50% yield reduction occurred at a shoot concentration of 3500 mg kg–1, which was reached at a soil solution concentration of 360 mg Mn L⁻¹ or a total Mn concentration in soil between 500 (low pH) and 2500 mg kg⁻¹ (high pH soil). Waterlogging of the soil during plant growth marginally increased Mn uptake in the high pH soil but did not have a significant effect on the total soil Mn-based toxicity thresholds. X-ray absorption near-edge structure spectroscopy (XANES) spectra were collected for unamended soils and for soils amended with MnCl2 near the 50% inhibition dose. The soils were incubated either at field capacity or were waterlogged for 7 d or 2 mo with or without addition of organic matter. Waterlogging had no effect on Mn speciation in the low pH soil (pH 4.7), in which Mn was mainly as Mn(II). In the unamended soils with pH > 6, waterlogging reduced Mn(III/IV) to Mn(II), and increased the solubility of Mn. However, in soils amended with MnCl₂, the added Mn remained for a large part as Mn(II), even under aerobic conditions, explaining why waterlogging had little effect on the toxicity of Mn. Addition of hay promoted reduction of Mn(III/IV)) while peat decreased reduction rates. This study showed that Mn toxicity can be related to the solubility of Mn, which is strongly dependent on pH and on kinetically controlled redox reactions.