Ion-conducting polymers (ionomers) are an important component of the heterogenous electrodes (catalyst layers, CL) in proton exchange membrane fuel cells (PEMFCs). In the CL, the nano-thin ionomer layer facilitates mass transport to and from the catalyst sites. Emerging chemistries have the potential to improve this mass transport by inserting additional acid groups to each sidechain or by modifying the backbone. This work aims to understand the impact of ionomer chemistry on the structure-property relationships relevant to fuel cells. Ionomer thin films (<100 nm) cast on planar supports model the CL ionomer. Film nanomorphology is characterized via in situ grazing-incidence x-ray scattering (GIXS); application-relevant properties, including hydration and proton conductivity, are probed via spectroscopic ellipsometry and electrochemical impedance spectroscopy, respectively. While both sidechain and backbone modifications lead to improvements in proton conductivity, the sidechain-modified ionomers show greater hydration and nanophase separation, and the backbone-modified ionomers show reduced hydration and nanophase separation, demonstrating the interplay between morphology, hydration, and film function. These results show that chemistry is a useful tool to tune thin film properties and provide insight to guide future ionomer design.