The membrane composed of carbon nanotube arrays may be widely used in biological molecular devices, image display area and optoelectronic devices. In this paper, the water permeability of the (11, 11) carbon nanotube arrays is simulated by using the SPC/E water model and the molecular dynamics program LAMMPS at 300 K. It is found that the distance between carbon nanotubes has a significant impact on water density distribution and the electric dipole moment orientation. Regardless of the distance between the neighboring tubes, water molecules will get into the nanotubes and form a double-layer cylindrical ring structure inside the nanotubes. However, water molecules can fill into the interstitial space of the nanotube array only when the nearest distance between the neighbor the tubes is greater than 3.4 Å, or the interstitial cross area becomes greater than 57.91 Å2. As the interstitial space increases, the structure of water molecules in the interstitial space will evolve from disconnected single-file chains to boundary-shared close-packing-like columnar circles. Meanwhile, the radius of the water ring inside the nanotube will increase and its boundary becomes more sharp due to the attractions from those water molecules filled in the interstitial space. Relative to the tube axis, the distributions of the water molecular electric dipole moments in the interstitial space depend upon water structures. Under the condition of single-file chain, the distribution exhibits a bimodal characteristic, which is very similar to the distribution of water dipole moments inside the nanotube. Whereas, for the boundary-shared close-packing-like water columnar circle, the distribution of dipole moments shows a unimodal characteristic and the peak corresponds to the angle 90°. This indicates that the preferred orientation of the water dipoles points to the direction perpendicular to the tube axis. These conclusions are helpful in the understanding of the water transport properties in carbon nanotube arrays.