In this work, we investigated the free energy barrier for transporting water molecules from one place to another. To properly address this issue, we considered a simple model system in which two separate compartments were connected via a subnanometer channel; all water molecules were initially in one compartment, and the other compartment was empty. Using umbrella sampling in molecular dynamics simulations, we calculated the free energy change for transporting all water molecules to the initially empty compartment. The free energy profile clearly indicated the presence of a free energy barrier, and the magnitude and shape of the barrier were dependent on the number of water molecules to be transported. To better understand the nature of the profile, we performed additional analyses on the potential energy of the system and hydrogen bonding between water molecules. Our study sheds light on a method for calculating the free energy of a transport system as well as the fundamental aspects of water transport.