It is well established that proton conductivity in fuel cell membrane materials such as Nafion decreases strongly with decreasing water content. Proton transport in almost dry membranes is thought to proceed through narrow channels. In the present work we investigate proton structure and dynamics in two narrow cylindrical pores, which differ by their radius and the spacing of SO3H groups inside the channel. Pores are modelled through eight CF3CF3 and four CF3SO3H entities in a helical arrangement. The water content λ (the ratio between the number of water molecules and the number of sulfonic acid groups) in the pores varies between 2.5 and 4.5. We observe a transition from the undissociated acid at very low λ through more or less localized H3O + entities to more delocalized H5O2 + entities for the investigated range of λ. In the narrower pore, where S–S distances vary in a more favourable range (between 6 and 8.5 Å) than in the wider pore, we find that the molecular mobility is significantly higher, even at a rather high density of water molecules inside the pore.