Colloidal Nafion morphology plays a critical role in determining the performance of fuel cells and electrolyzers. While small-angle neutron scattering (SANS) studies previously described Nafion in liquid media as dispersed cylinders, the analysis remains nonunique with multiple possible morphological descriptions of the data. Here, using SANS and all-atomistic molecular dynamics, we confirm that Nafion morphology in liquid media differs substantially depending on dispersing agent and dispersion method. H+ Nafion dispersed in N-methyl pyrrolidone forms swollen cluster particles with physically cross-linked ionic groups. Scattering profiles from dispersed Nafion membrane have a large structure factor feature not observed for redispersed Nafion D-521. H+ Nafion dispersed in water has a highly elongated cylindrical morphology (radius = 10 ± 1.5 Å, height = 358 ± 4.7 Å) with fully dissociated and solvated sulfonic acid groups on the particle wall. These results highlight an important discrepancy between the methods of preparing Nafion dispersions and the use of simplified analysis techniques to describe Nafion morphology.