Application of nanoparticles in the subsurface typically requires the use of surface coatings to maintain stability in dispersion and to provide particular functionality. However, the presence of surface coatings may hinder or mask properties of the bare nanoparticle cores, which may be a concern in nuclear magnetic resonance (NMR) applications. In this study, we used different amounts of 3-aminopropyltriethoxysilane (APTES) coating on Fe3O4 magnetic nanoparticles (A-MNPs). We measured the longitudinal relaxation time (T1) values of those A-MNPs suspensions, and computed and compared the surface relaxivities of A-MNPs with different amounts of APTES coating. Our results showed that when the mass percentage of APTES coating increased from 1.60 to 4.22 wt%, the A-MNPs’ surface relaxivity decreased by 26.1%. To determine the surface relaxation mechanism(s), we also used various volume fractions of D2O to dilute A-MNP dispersions to two concentrations: 0.01 and 0.002 g/L Fe. In the final mixtures, the volume fractions of D2O were fixed as 0-, 30-, 50-, and 70-vol%. The NMR measurements indicated that, at relatively high Fe concentration (0.01 g/L), electron-proton interaction dominates surface relaxation, and the hydrogen atoms in the APTES did not significantly alter the surface relaxation mechanism of the nanoparticles. At a lower Fe concentration (0.002 g/L), proton-proton relaxation, due to the APTES, also played a role in the overall relaxation mechanism on nanoparticle surfaces. A-MNPs with more APTES coating showed lower apparent surface relaxivities with higher D2O volume fractions in the mixture, indicating a greater amount of proton-proton relaxation on the nanoparticle surfaces.