Plant cell walls are abundant sources of materials and energy. Nevertheless, cell wall nanostructure, specifically how pectins interact with cellulose and hemicelluloses to construct a robust and flexible biomaterial, is poorly understood. X-ray scattering measurements are minimally invasive and can reveal ultrastructural, compositional, and physical properties of materials. Resonant X-ray scattering takes advantage of compositional differences by tuning the energy of the incident X-ray to absorption edges of specific elements in a material. Using Tender Resonant Xray Scattering (TReXS) at the calcium K-edge to study hypocotyls of the model plant, Arabidopsis thaliana, we detected distinctive Ca features that we hypothesize correspond to previously unreported Ca-Homogalacturonan (Ca-HG) nanostructures. When Ca-HG structures were perturbed by chemical and enzymatic treatments, cellulose microfibrils were also rearranged. Moreover, Ca-HG nanostructure was altered in mutants with abnormal cellulose, pectin, or hemicellulose content. Our results indicate direct structural interlinks between components of the plant cell wall at the nanoscale and reveal mechanisms that underpin both the structural integrity of these components and the molecular architecture of the plant cell wall.