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Abstract Water‐mediated proton conductivity in nanoporous materials is influenced by channel water ordering and the hydrophobicity/hydrophilicity of interior walls, making metal‐organic nanotubes (MONTs) useful systems for exploring these relationships due to their high crystallinity and tunable hydrophobicity. In the current study, electrochemical impedance spectroscopy is utilized to explore the proton conductivity on two metal organic nanotubes (UMONT and Cu‐LaMONT) with weak hydrophobic behavior that possess extended water networks within the 1‐D channels. Measurements performed at 95% RH and 20 °C indicate values of 1.63 × 10⁻⁴S cm⁻¹for UMONT and 3.80 × 10⁻⁴S cm⁻¹for Cu‐LaMONT, which is lower than values for walls with acidic, hydrophilic functional groups or nanotubular materials with strictly hydrophobic behavior. Proton conductivity decreases sharply with lower humidity, with Cu‐LaMONT being more sensitive to humidity changes. At low temperatures, UMONT outperforms LaMONT due to its well‐established hydrogen bonding network and hydrophobic interior. The anisotropic nature of proton conduction is also confirmed through pelletized powder sample analysis, emphasizing that the conductivity occurs through the water networks located within the 1‐D MONT channels. These findings emphasize the importance of understanding water–pore interactions and the resulting proton conductivity mechanisms to understand complex systems and design advanced materials.