In this work we have analyzed the influence of various factors on the transverse relaxation times T2 of water protons in suspension of magnetic nanoparticles. For that purpose we developed a full molecular dynamics force field which includes the effects of dispersion interactions between magnetic nanoparticles and water molecules, electrostatic interactions between charged nanoparticles and magnetic dipole–dipole and dipole–external field interactions. We also accounted for the magnetization reversal within the nanoparticles body frames due to finite magnetic anisotropy barriers. The force field together with the Langevin dynamics imposed on water molecules and the nanoparticles allowed us to monitor the dephasing of water protons in real time. Thus, we were able to determine the T2 relaxation times including the effects of the adsorption of water on the nanoparticles’ surfaces, thermal fluctuations of the orientation of nanoparticles’ magnetizations as well as the effects of the core–shell architecture of nanoparticles and their agglomeration into clusters. We found that there exists an optimal cluster size for which T2 is minimized and that the retardation of water molecules motion, due to adsorption on the nanoparticles surfaces, has some effect in the measured T2 times. The typical strengths of the external magnetic fields in MRI are enough to keep the magnetizations fixed along the field direction, however, in the case of low magnetic fields, we observed significant enhancement of T2 due to thermal fluctuations of the orientations of magnetizations.