In the framework of a protein–ligand-fishing strategy to identify proteins that bind to trans- resveratrol, a natural phenolic compound with pharmacological benefits, we have developed magnetic nanoparticles covalently linked to trans -resveratrol through three different derivatives and examined their aggregation behavior in aqueous solution. The monodispersed magnetic core (18 nm diameter) with its mesoporous silica shell (93 nm diameter) exhibited a notable superparamagnetic behavior useful for magnetic bioseparation. The hydrodynamic diameter, deduced from dynamic light scattering analysis, of the nanoparticle increased from 100 to 800 nm when the aqueous buffer changed from pH 10.0–3.0. A size polydispersion occurred from pH 7.0–3.0. In parallel, the value of the extinction cross section increased according to a negative power law of the UV wavelength. This was mainly due to light scattering by mesoporous silica, whereas the absorbance cross section remained very low in the 230–400 nm domain. The three types of resveratrol-grafted magnetic nanoparticles exhibited similar scattering properties, but their absorbance spectrum was consistent with the presence of trans -resveratrol. Their functionalization increased their negative zeta potential when pH increased from 3.0 to 10.0. The mesoporous nanoparticles were monodispersed in alkaline conditions, where their anionic surface strongly repulsed each other but aggregated progressively under van der Waals forces and hydrogen bonding when negative zeta potential decreased. The characterized results of nanoparticle behavior in aqueous solution provide critical insight for further study of nanoparticles with proteins in biological environment.