Understanding the properties of liquid confined in extended nanospaces (10-1000 nm) is crucial for nanofluidics. Because of the confinement and surface effects, water may have specific structures and reveals unique physicochemical properties. Recently, our group has developed a super resolution laser-induced fluorescence (LIF) technique to visualize proton distribution with the electrical double layer (EDL) in a fused-silica extended nanochannel (Kazoe, Y.; Mawatari, K.; Sugii, Y.; Kitamori, T. Anal. Chem.2011, 83, 8152). In this study, based on the coupling of the Poisson-Boltzmann theory and site-dissociation model, the effect of specific water properties in an extended nanochannel on formation of EDL was investigated by comparison of numerical results with our previous experimental results. The numerical results of the proton distribution with a lower dielectric constant of approximately 17 were shown to be in good agreement with our experimental results, which confirms our previous observation showing a lower water permittivity in an extended nanochannel. In addition, the higher silanol deprotonation rate in extended nanochannels was also demonstrated, which is supported by our previous results of NMR and streaming current measurements. The present results will be beneficial for a further understanding of interfacial chemistry, fluid physics, and electrokinetics in extended nanochannels.