Synthetic molecular crystals with one-dimensional nanoporous channels containing H 2 O molecules act as model systems for pores such as aquaporin-1 in cell membranes. The structural characteristics of water molecular clusters (WMCs) were investigated using X-ray crystal analysis of {[Ni II -(cyclam)] 3 (TMA) 2 ¢3534 H 2 O} n (2) (TMA: trimesate, cyclam: 1,4,8,11-tetraazacyclotetradecane) in a closed glass capillary to adjust the saturated humidity. The structural phase transition of WMCs with temperature depends only on the H 2 O structures around the centre, not on those in the primary hydrate layer nearest to the outer wall. The centre of a WMC was filled with H 2 O molecules under saturated humidity conditions; however, in air, the WMC had a nanotube-like structure with a vacant space. Thus, the centre portion of a WMC probably contains volatile and mobile H 2 O molecules. Therefore, we investigated the rapid proton conductivity using alternating current impedance and microwave spectroscopy and also carried out a transpiration experiment for transferring the mobile H 2 O molecules. The microwave spectroscopy results for 2 indicated no isotope effect, which would be observed by the rapid motion of H 2 O molecules without the breaking of hydrogen bonds between two site-disordering positions above the phase transition temperature. The results indicated reasonable water transpiration ability of the single crystal through its nanochannels; this property can be useful as a working principle to understand applications such as the desalination of seawater.