Modification of iron oxide nanoparticles (NPs) synthesized by high temperature solvothermal routes is carried out using two silanes: (i) N-(6-aminohexyl)-aminopropyltrimethoxysilane (AHAPS) where only one end of the molecule reacts with the surface Fe–OH groups and (ii) 3-(triethoxysilyl)propylsuccinic anhydride (SSA) where both ends are reactive with Fe–OH. Depending on the NP synthesis protocol, the amount of surface OH groups on the NPs may differ, however, for all the cases presented here, the comparatively low OH group density prevents a high density of AHAPS coverage, yielding NP aggregates instead of single particles in aqueous solutions. Alternatively, use of SSA containing two terminal functionalities, anhydride and siloxy, which are both reactive towards the NP surface, results in the formation of discrete dense polymeric shells, providing stability of individual NPs in water. The mechanism of the SSA shell formation is discussed. The evolution of the chemical transformations leads to shells of different thickness and density, yet this evolution can be halted by hydrolysis, after which the NPs are water soluble, negatively charged and exhibit excellent stability in aqueous media.