Transportation of water molecules in a carbon nanotube based on an energy pump concept is investigated by molecular dynamics simulations. A small portion of the initially twisted wall of a carbon nanotube is employed to function as an energy pump for possible smooth transportation of water molecules. The momentum and resultant force on a water molecule and the corresponding displacement and velocity of the molecule are particularly studied to disclose the transportation process. The efficiency of the transportation is found to be dependent on the size of the energy pump. Once the process for the transportation of one molecule is elucidated, transportations of 20 water molecules are simulated to investigate the effect of the environmental temperature and fluctuations in the nanotube channel on the transportation. It is revealed that the accelerated period of multiple water molecules is longer than that in the transportation of a single water molecule. In addition, the fluctuations in the nanotube wall due to the buckling propagation and a higher environmental temperature will all lead to obvious decreases in the water velocity and hence retard the transportation process.