The structure of perhydropolysilazane (PHPS)-derived silica (PDS) waterproof thin layers synthesized by curing at 60 °C for 1 h and allowed to stand for 48 h at 20 °C on various kinds of substrates was studied. Neutron reflectivity (NR) analysis suggested that uniform PDS thin layers were synthesized on the substrates, and the density of the layers varied depending on the type of substrate. Additionally, since the change in PDS density is correlated with the pK_a value of the OH group on the substrate, it can be suggested that the acidity of the substrate would be one of the main factors determining the density of the coated PDS thin layers. For the water penetration structure study, NR analysis revealed that the depth of water penetration into the PDS layers was below 500 Å, and the hydration number of the SiO₂ molecule was estimated to be 8.0–9.0. From these results, we concluded that water penetration occurred by the formation of water-pool structures in the PDS layers, and the randomly formed nano-air holes lead to a reduction in the probability of water penetration into the deep regions of the PDS layers.