Extensive characterizations of the water, ionic cluster structure, and ionic conductivity of Aciplex((R)) S1001 (polyperfluorosulfonic acid: PFSA membrane) were carried out using IR and SAXS measured under varied relative humidity conditions. States of the water in the membrane were classified into two types: free water and bound water. Each type of water was found to affect the ionic conductivity of the membrane in a different way; particularly, the presence of the free water was necessary for the conductivity. Below the relative humidity of 30%RH, all the water contained in the membrane was bound water. And above 60%RH, a significant increase in the free water was observed. The change of the states of water may be caused by an alteration of the ionic cluster structure when individual clusters appeared to form a connected ionic cluster network. This water behavior, as well as the morphological change of the supermolecular structure of the membrane, accounts for the dramatic increase in the conductivity at 60%RH or above.