Understanding a biomaterial's structural and hydration dynamics is essential for its development and applications in tissue regeneration. In this study, collagen-hyaluronic acid (HA) scaffolds were analyzed utilizing Nuclear Magnetic Resonance (NMR) techniques to elucidate how different cross-linking conditions influence the internal architecture and interaction with solvents in these scaffolds. The scaffolds were fabricated using 3D printing and cross-linked with 1,4-butanediol diglycidyl ether (BDDGE), a process known to impact their mechanical properties. We gained insights into the microstructural organization and hydration behavior within the scaffolds when exposed to water and ethanol by employing proton relaxation and diffusion measurements. To better understand the system's performance, static and dynamic experiments were performed. Our results indicate that the degree of cross-linking affects the scaffold's ability to retain water, with higher cross-linking leading to more rigid structures. This also altered the hydration dynamics mainly due to a difference in the diffusion of water within the scaffold. In addition, the anisotropy of the collagen fibers also decreases with the cross-linking. Ethanol, a less polar solvent, provided a contrasting environment that further revealed the structural dependencies on the cross-linking density. The study's findings contribute to a deeper understanding of how the structure and morphology affect the functionality of collagen-HA scaffolds, offering critical information for optimizing their design for specific biomedical applications, such as soft tissue regeneration. Our experiments show how NMR is a valuable tool to provide information on dynamic processes not only in collagen-HA scaffolds but also in many biocompatible polymeric samples. The outcomes of this research provide a foundation for future work aimed at tailoring scaffold properties to enhance their performance in clinical settings, ultimately advancing the field of tissue engineering.