Commercially available perfluorosulfonic acid polymers are commonly used as proton-exchange membranes (PEMs) in electrochemical devices. Nanoscale water channels lined with sulfonic acid groups are a key feature of these materials that we recently reproduced in a series of fluorine-free polymers. We previously used all-atom molecular dynamics simulations to reveal details about the water channels in selected polymers at a few levels of hydration. In this paper, we quantitatively compare the nature of the water channels found by MD with experimental small-angle X-ray scattering (SAXS) data. First, we reconstructed three-dimensional real-space nanoscale morphologies from SAXS data using Gaussian random fields. Next, we developed methods to characterize the water channels within these reconstructions, specifically extracting the characteristic lengths, cluster analysis, channel width distributions, and fractal dimensions. Finally, we report good agreement between all-atom MD simulations and the morphologies reconstructed from SAXS data. These results demonstrate the value of the Gaussian random fields method to rapidly, reliably, and quantitatively analyze nanoscale morphologies in nanophase-separated soft materials without long-range order.