Physicochemical properties of the nanostructured complex systems, formed between the deferrioxamine B (DFO) siderophore ligand and Zr(IV), Hf(IV), or Fe(III) metal ions at the gold−thiol electrode surface, are determined by different surface, electrochemical, and solution techniques, and the systems are characterized. The results obtained from separate experiments show that the DFO can accumulate and complex the M ions [M: Fe(III), Hf(IV), or Zr(IV)] on the gold−mercaptopropionic acid (Au−MPA) surface efficiently but with different affinities as Zr(IV) > Hf(IV) > Fe(III), leading to different surface morphologies and organizations, and structural diversity of the Au−MPA−DFO−M complexes as Fe(III) > Hf(IV) > Zr(IV). Furthermore, the Fe(III) ions of the Au−MPA−DFO−Fe(III) surface are replaced rapidly by both Hf(IV) and Zr(IV) ions but with different kinetics; the replacement of Zr( IV) is ∼three times faster than that of Hf(IV) at highly acidic solution. Thus, the DFO can be used to identify and differentiate the behaviors of these important heavy metal ions. To our knowledge, this is one of the few cases in which Hf(IV) and Zr(IV) ions show different behaviors. The results of this study are important and can improve our physicochemical insights into the behavior of these ions in conjunction with siderophores, regarding the natural and industrial environments, metal refinery and nuclear power plants, human biological systems, soil contamination, agricultural products, and foods.