This work reports on the effects of titanium dioxide (TiO2) and magnesium oxide (MgO) nanofillers modified with polar silane coupling agents (SCA) on the dielectric response of polypropylene (PP) nanocomposites, in the presence of water molecules. Thermogravimetric analysis demonstrates that the surface structure of the SCA layer between TiO2 and MgO is significantly different, since the SCA graft density of MgO is 10 times higher than for TiO2. Surface modified nanofillers tend to agglomerate and that the distribution is determined by the polarity of the surface functional groups. Agglomerations in methacrylate systems are similar in size to those found in untreated samples (3-5 µm), while those with amino functional groups are reduced to 1-2 µm. Nanoparticles also act as nucleating agents, which increases the crystallization temperature by 7-8 °C compared to neat PP. The measured increase in relative permittivity in the composites is attributed to absorbed water. Surface modification significantly reduces this increase, especially in MgO samples. Relaxation peak frequencies vary, depending on the water bonding states, due to differences in polarities of the respective surface functional groups. Two overlapping dielectric mechanisms of dipolar and interfacial relaxation can be detected, especially at low frequencies (20 µHz) in TiO2 samples. Ethoxy-modified samples containing amino functional groups have the lowest dielectric permittivity under humid conditions.