The fluorinated ionomer Nafion is a material that provides efficient proton conducting membranes for application in important technological areas such as hydrogen fuel cells. Despite being carefully studied for the 20 years or so since it was first discovered by the DuPont company, the microscopic mechanisms for proton transport in this polymer are still only poorly understood. Muon spectroscopy has great potential to contribute to the further understanding of this polymer in two ways, firstly by making use of the muon as a mimic of the proton in the system to study the proton dynamics and secondly by making use of the fingerprint relaxation function of a muon interacting with one or more F atoms. This will allow unique information to be obtained on the partitioning of the muon (i.e. the mobile proton) between the F-free ionic regions and and the F-rich polymeric framework regions.