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Controlling nanoparticle transport in hydrophilic electrospun systems remains challenging due to rapid aqueous dissolution and unrestricted diffusion pathways. In this study, a bilayer electrospun nanofibrous platform composed of hyaluronic acid/polyvinyl alcohol (HA/PVA) and copper nanoparticle-loaded polyvinyl alcohol (PVA/CuNP) was engineered to investigate how thermal post-treatment regulates microstructure and transport behavior. Layer-specific thermal stabilization (150°C for HA/PVA; 110°C for PVA/CuNP) induced polymer chain rearrangement and network densification while preserving fiber morphology, as confirmed by SEM analysis (average fiber diameters: 223 ± 29 nm untreated; 208 ± 25 nm treated). Thermal treatment significantly enhanced aqueous stability, reducing degradation to ∼1.27% after 24 h, while maintaining high swelling capacity (up to 608 ± 5%). Thermogravimetric analysis confirmed a CuNP loading of 14.58%, and release studies demonstrated sustained nanoparticle release (∼28.4% over 24 h) without burst behavior. The results indicate that nanoparticle transport is governed primarily by processing-induced microstructural compactness and diffusion tortuosity rather than nanoparticle loading alone. This work establishes a processing-microstructure-transport design principle for regulating stability and mass transport in multilayer electrospun polymer-nanoparticle systems. Bilayer electrospun HA/PVA nanofibers were engineered to achieve controlled microstructural features Green-synthesized copper nanoparticles were uniformly incorporated into PVA nanofibers. Optimized thermal treatment yielded stable, bead-free bilayer nanofibrous mats. The nanofibers exhibited high swelling capacity and controlled degradation behavior. Sustained copper nanoparticle release was achieved over a 24-hour period.