This article is focused on the theoretical and experimental study of the interactions between the perchlorate anions and the cations of cobalt ferrite magnetic nanoparticles prepared by a co-precipitation method. The magnetic nanoparticles with surface modified using perchloric acid were stabilized in aqueous dispersion based upon the predominant electric repulsive forces between the coated nanoparticles, balancing the magnetic dipole-dipole attraction. Quantum chemical modeling has revealed the physical-chemical properties of perchlorate anion (electric charges, dipole moment, and energies of frontier orbitals) that suggests the ability to interact with both nanoparticle metal cations and surrounding water molecules. Microstructural investigations by scanning electron microscopy, X-ray diffractometry, and vibrating sample magnetometry revealed crystallinity and granulation of the suspended ferrophase, thus confirming the adequate surface coating with perchlorate anions. The nanotoxicity study, carried out on agricultural plantlets in early ontogenetic stages has revealed differences in the photosynthesis pigment concentrations induced by the magnetic nanoparticle supply.