Small-angle neutron scattering with contrast variation and transmission electron microscopy have been used to investigate the nanostructure of films cast from diblock copolymer solutions. The polymers are composed of a fluorocarbon block and a sulfonated polystyrene block, where the length and degree of sulfonation of the polystyrene segment have been controlled. This study shows that these films possess structure at two length scales: phase separation at length scales of the order of 40 nm due to the immiscibility of the two polymer blocks and substructure within the sulfonated polystyrene domains due to segregation of the hydrated ionic groups and the hydrophobic polystyrene chains. The longer length scale morphology is well-ordered for diblocks containing long and partially sulfonated polystyrene blocks whereas the short and fully sulfonated polystyrene blocks give rise to a more disordered structure.