Hydrogel materials are crucial in many applications due to their versatility and ability to mimic biological tissues. While manipulating bulk hydrogel cross-link density, polymer content, chemical composition, and microporosity has been a main approach to controlling hydrogel rigidity, altering the internal organization of hydrogel materials through chain intermixing and stratification can bring finer control over hydrogel properties, including mechanical responses. We report on altering the mechanical properties of ultrathin poly(methacrylic acid) (PMAA) multilayer hydrogels by controlling the internal organization of the PMAA network. PMAA multilayer hydrogels were synthesized by cross-linking PMAA layers in poly(N-vinylpyrrolidone) (PVPON)/PMAA hydrogen-bonded multilayer templates prepared by dipped or spin-assisted (SA) layerby-layer assembly using sacrificial PVPON interlayers with molecular weights of 40,000 or 280,000 g mol −1 . The effect of PVPON molecular weight on PMAA hydrogel stratification and network swelling and hydration was assessed by in situ spectroscopic ellipsometry and neutron reflectometry (NR). In a new NR modeling of polymer intermixing, we have inferred nanoscopic structure and water distribution within the ultrathin-layered films from measured continuum neutron scattering length density (SLD) and related those to the mechanical properties of the hydrogel films. We have found that hydrogel swelling, the number of water molecules associated with the swollen hydrogel, and water density within the SA PMAA hydrogels can be controlled by choosing low-or high-M w PVPON. While cross-link densities determined by ATR-FTIR were similar, greater swelling and hydration at pH > 5 were observed for SA PMAA hydrogels synthesized using higher-M w PVPON. The enhanced swelling of these SA hydrogels resulted in softening with a lower Young's modulus at pH > 5 as measured by colloidal probe atomic force microscopy (AFM). The effect of PMAA layer intermixing on hydrogel mechanical properties was also compared for dipped and SA (PMAA) multilayer hydrogels of similar thickness and cross-linking degree. Despite similar values of gigapascal-range Young's modulus for dry PMAA multilayer hydrogel films, an almost twice greater softening of the SA (PMAA) hydrogel compared to that prepared by dipping was observed, with Young's modulus values decreasing to tens of megapascals in solution at pH > 5. Our study demonstrates that, unlike simply changing bulk hydrogel cross-link density, programming polymer network architecture via controlling the nanostructured organization of SA PMAA hydrogels enables selective modulation of the cross-link density within hydrogel strata. Control of polymer chain intermixing through hydrogel stratification offers a framework for synthesizing materials with finely tuned hydrogel internal structures, enabling precise control of such physical properties as the internal architecture, hydrogel swelling, surface morphology, and mechanical response, which are critical for the application of th...