In this book the authors focus on the ion and water transport characteristics in Nafion and other perfluorinated ionomer membranes that are recently attracting attention in various fields such as water electrolysis, mineral recovery, electrochemical devises and energy conversion. Methodology of measurements and data analysis is first presented that enables basic characterisation of transport parameters in the perfluorinated ionomer membranes. Cation exchange isotherm data are collected in binary cation systems, with the aim to see the behaviours of cationic species that exist with H+ in the membrane. Water transference coefficients, ionic transference numbers, ionic mobilities and other membrane transport parameters are measured in single and mixed counter cation systems using electrochemical methods. Diffusion coefficients of water and cations are also measured by pulsed-field-gradient spin-echo NMR (PGSE-NMR) at various temperatures in different kinds of perfluorinated ionomer membranes. The results are discussed in two perspectives. One is to predict the hydration state in perfluorosulfonated ionomer membranes in relation to the possible degradation of performances in fuel cells under contaminated conditions with foreign cations. An analytical formulation of membrane transport equations with proper boundary conditions is proposed, and using various parameters of membrane transport, a simple diagnosis of water dehydration problem is carried out. This analysis leads one to an effective control of fuel cell operation conditions, especially from viewpoint of proper water management. The others are to elucidate the ion and water transport mechanisms in the membrane in relation to polymer structures (e.g., different ion exchange capacity), and to propose a new design concept of polymer electrolyte membranes for fuel cell applications. Additionally for this purpose methanol and other alcohols are penetrated into the membrane, and alcohol permeability, membrane swelling, ionic conductivity and diffusion coefficients of water and CH3 are measured systematically for various kinds of membranes to cope with the problem of methanol crossover in direct methanol fuel cells (DMFCs).It is found that in order to realise a high ionic conductivity in the membrane, one should aim at a polymer structure through molecular design that takes into account the relative size of ions with a hydration shell against the size and atmosphere of ionic channels. For DMFC, a partially cross-linked polymer chain with high degree of hydrophilic ion transport paths based on phase-separated structures is recommended. Various possibilities of such polymer electrolytes are discussed.