We study the assembly of magnetite nanoparticles in water-based ferrofluids in wetting layers close to silicon substrates with different functionalization without and with an out-of-plane magnetic field. For particles of nominal sizes 5, 15, and 25 nm, we extract density profiles from neutron reflectivity measurements. We show that self-assembly is only promoted by a magnetic field if a seed layer is formed at the silicon substrate. Such a layer can be formed by chemisorption of activated N-hydroxysuccinimide ester-coated nanoparticles at a (3-aminopropyl)triethoxysilane functionalized surface. Less dense packing is reported for physisorption of the same particles at a piranha-treated (strongly hydrophilic) silicon wafer, and no wetting layer is found for a self-assembled monolayer of octadecyltrichlorosilane (strongly hydrophobic) at the interface. We show that once the seed layer is formed and under an out-of-plane magnetic field further wetting layers assemble. These layers become denser with time, larger magnetic fields, higher particle concentrations, and larger moment of the nanoparticles.