Molecular dynamics simulations were performed to study the movement of water molecules and protons in two pores : a small pore of radius 9.36 Angstrom and a larger one of radius 12.24 Angstrom. Inside the ionic solution the wall charge densities are approximately -0.1 C/m(2) and -0.2 C/m(2). Water and proton distributions in the pore are affected strongly by the water content and the wall charge density. In the case of low wall charge density, if there is a sufficient number of water molecules in the pore, the protons are strongly hydrated to the water molecules and do not directly contact the wall. In the case of high wall charge density, most of the protons are attracted to the wall. Then, the wall charge and the absorbed protons together behave like a weakly charged wall. We found that the Poisson-Boltzmann theory fails to predict the proton distribution in these pores. The calculated electroosmotic drag coefficient, proton diffusion coefficient and pore conductance are compared with the simulation results for the Nafion-117 membrane. This study suggests that if the Nafion-117 membrane is modeled as a large number of identical cylindrical pores, the effective wall charge densities in the pores will never reach the value of -0.2 C/m(2).