Molecular dynamics simulations with anion exchange membranes (alkyl trimethyl ammonium grafted onto polysulfone) are performed to investigate the influence of the spacer length on the transport properties, on the molecular exchange mechanisms between the functional group and the aqueous phase and on the hydrogen bond network. This is especially insightful that in this work the hydration number is small. In this condition the aqueous phase must be thought as an assembly of small clusters. The results show an unexpected dependence of the water and hydroxide (OH) diffusivity on the temperature and the water uptake. The distribution of the cluster size bonded to OH explain partially the OH diffusivity. “Hopping” and “caging” motions are observed with the self-part of the Van Hove functions even at high temperature. The characteristic time of the survival probability correlation function around the functional groups is a decreasing function of the alkyl length.