Weathering of peridotites and serpentinites leads to the formation of ultramafic soils characterized by several peculiar properties such as low Ca/Mg ratios and elevated concentrations of Ni, Cr, and Co. The aim of our study was to investigate the effects of Ca²⁺ and Mg²⁺ on seed germination in the environment that mimic ultramafic and non-ultramafic soils. We hypothesized that Ca and Mg alleviate toxicity of Ni, Cr, and Co in relation to seed germination and root length. Regardless of concentration, metal salts inhibited seed germination and root growth for almost all studied plant species compared to control. An increase in germination was observed in treatments containing high concentrations of Ni²⁺ and Co²⁺ with the addition of Ca²⁺ and Mg²⁺. Roots of plants had greater length in high Ni²⁺ and Co²⁺-treatments with Ca²⁺ and Mg²⁺ in relation to metal treatments without the addition of Ca²⁺ and Mg²⁺. In low-content metal treatments with Ca²⁺ and Mg²⁺, roots had similar or smaller lengths compared to metal treatments. Our results demonstrate that Ca²⁺ and Mg²⁺ alleviate toxicity of Ni²⁺ and Co²⁺ during seed germination and root growth under conditions simulating ultramafic soils. Therefore, in soils derived from ultramafic rocks enriched in Ca, an increase in germination and root growth is expected as opposed to soils occurring on Ca-poor ultramafic rocks. In non-ultramafic soils containing relatively low amounts of Ni, Cr, and Co, the roles of Ca and Mg are negligible.