One of the most significant environmental challenges in the twenty-first century is heavy metal pollution. The potential use of freshAzolla pinnatato alleviate the toxic effects of Cd and Co on the germination measurements of wheat seeds (Triticum aestivumL.) and the biochemistry of seedlings was studied. Two concentrations (80 and 100 mg L−1solutions) of CdNO3and CoCl2were used before and after treatment withA. pinnata. The highest removal efficiency (RE) byA. pinnatawas obtained on the fifth day, with a Cd RE = 55.9 and 49.9% at 80 and 100 mg L−1, respectively. Cadmium and cobalt solutions reduced the germination percentage, and the measured variables of wheat seeds meanwhile increased the radicle phytotoxicity. In contrast, the presence ofA. pinnatain the germination medium increased all the measured variables and decreased radicle phytotoxicity. At 80 and 100 mg L−1, Cd significantly reduced the fresh and dry biomass, and height of wheat seedlings after 21 days of cultivation compared to Co. Cadmium and high concentrations of cobalt increased the contents of H2O2, proline, MDA, phenolic, and flavonoid compounds. The application of treated Cd and Co solutions byA. pinnatashowed a decrease in H2O2, proline, phenolic, and flavonoid compounds levels accompanied by a reduction in catalase and peroxidase activities compared to the control. This study showed the positive role ofA. pinnatain alleviating the metal impacts, particularly Cd, on the seedling growth of wheat and its germination.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11356-023-27566-1.