The present studies shed light on the continuum breakdown of water confined in nanotubes of different materials and diameters. The structure and hydrodynamics of water confined in nanotubes of carbon (CNT), boron nitride (BNNT), silicon carbide (SiC), and silicon nitride (SiNT) of different chirality indices were analyzed to examine the potential nanomembrane material for water purification. According to our findings of the contact angle with water, BNNTs are more hydrophobic than CNTs, and silica nanotubes are hydrophilic. The higher permeability of water was observed through CNTs and BNNTs in comparison to silica nanotubes. Nearly flat velocity profiles indicated continuum breakdown at the nanoscale. Also, the trend for viscosity and diffusion coefficient did not follow the Stokes−Einstein relation, indicating continuum breakdown. The results demonstrated the connectivity of microscopic diffusion with the macroscopic permeation flux, which might be important information for the theoretical investigation of the suitable operational regime in reverse osmosis. Essentially, the continuum breakdown due to freezing of water was seen to be diminished with an increase in temperature. The results showed characteristic changes in the density profile, diffusion coefficient, velocity autocorrelation functions, density of state functions, and thermodynamic entropic components (evaluated using the two-phase thermodynamic method) of permeating water molecules. Importantly, our results reflect that the continuum breakdown observed for water confined in smaller nanotubes is true only at temperatures below 400 K due to the ice-like dense structure of water molecules. Once the entering water molecules can gain energy to compensate for the loss of H bonds, the conventional fluid dynamics relations can be well applied to estimate the hydrodynamics of confined water.