Nanofluids are produced by suspending different solid nano-size materials (metal and nonmetal) in a base liquid and are often used in energy systems to increase thermal performance and heat transfer rate. The main problem observed in nanofluids used in heat transfer applications is their instability. Researchers have developed and proposed some solutions to obtain stable nanofluids. One of the most important solutions, is the nanoparticles surface modification method. In this work, Fe3O4 nanoparticles were subjected to chemical processes and their surfaces were modified. Three different modified nanoparticles were synthesized, which are Fe3O4@SiO2@Si(CH2)3-IM [Cl], Fe3O4@Si(CH2)3-IM [Cl], and Fe3O4@SiO2&Si(CH2)3-IM [Cl] nanoparticles. The nanofluids were prepared in 0.2% Vol. fraction by using the produced particles in base fluid which was distilled water, and stability of nanofluids were observed for 3 months. Nanofluids were subjected to ultrasonication for 3.5 h to obtain homogeneous nanofluid. Not modified water-based Fe3O4 nanofluid completely collapsed in approximately 1 week. In modified nanofluids, although sedimentation occurred, it was observed that a certain amount of the particles remained suspended even after 3 months. The most important analyses in this study are Scanning Electron Microscope, X-Ray Diffraction, and Transmission Electron Microscope.