In this study, using silica modified nanoparticles Fe3O4/APTES as a model system, we explored two techniques for the dispersion of pre-formed nanoparticle suspensions into stable fractions, according to zeta potentials and hydrodynamic diameters. Two different techniques for dispersing silica MNPs in terms of their zeta potential and hydrodynamic diameter were reported and compared. Magnetic stirring was revealed to provide a good approach for the oxygen-sensitive dispersion of iron-containing nanoparticles, and it was efficient in terms of the loading capacity of functional humic substances, due to surface charging. The sonication-based method resulted in a low loading capacity, likely due to high temperature and pressure in the cavities formed at the interfaces, which induced breakage of the silica shell. The achieved data also confirmed that a electrophoretic mobility technique can be applied to predict the loading capacity for polyelectrolytes such as humic preparations.