Characterization of the internal morphology of thin film composite membranes used in reverse osmosis (RO) is a prerequisite for understanding the connection between microstructure and water transport properties and is necessary for the design of membranes with improved performance. Here, we examine a series of fully aromatic polyamide active layers of RO membranes that vary in crosslinking using a combination of resonant soft X-ray scattering (RSoXS), transmission electron microscopy (TEM), and atomic force microscopy (AFM). Analysis of RSoXS profiles reveals a correlation between membrane structure and crosslinking density. Through a combination of scattering contrast calculations, TEM, and AFM micrographs, we assign the dominant contribution to RSoXS data as either surface roughness or chemical heterogeneity, depending on the X-ray energy used. Altogether, our results demonstrate the utility of soft X-ray scattering to examine the microstructure of water filtration membranes.