It was found, the following ions of heavy metal: Ru, Rh, Pd, Ag, Os, Ir, Pt or Au are aggregated in humic acids. This gave an idea to create a tool that would detoxify soil (contaminated by heavy metals) by phytoremediation using the peat in suitable reaction composition. In the work nanoparticles with the use of humic/fulvic acid and silver, zirconium and copper have been produced and they have been analyzed by Nanoparticle Tracking Analysis, Dynamic Light Scattering, Scanning Electron Microscopy and Transmission Electron Microscopy methods. Moreover, molecular modeling of fulvic acid and humic acid have been performed with the use of DFT methods. The fulvic acid molecule forms only salt with the tested metal ions. The structure of humic acid molecule allows the coordination of the metal ion by means of three single bonds. It results in formation of the specific conformation of molecule with “the window” which diameter is about 7.3 Å and depends on the size of tested metal ion. This molecule conformation is responsible for the metal ion catching. The modeling of humus acids allowed to determine the most stable conformation, the places of potential attachment, and help in visualization the model of the obtained nanoparticle.