Aggregation of the polydopamine (PDA) molecular building blocks at the air/water interface leads to obtaining large surface nanometric-thin films. This mechanism follows two possible pathways, namely, covalent or non-covalent self-assembly, which result in a different degree of structure order and, consequently, different structural properties. Control of this mechanism could be vital for applications that require true self-support PDA free-standing films, for example, electrochemical sensing or membrane technology. Here, we are considering the impact of boric acid (BA) and Cu2+ ions on the mentioned mechanism exclusively for the free-standing films from the air/water interface. We have employed and refined our own spectroscopic reflectometry method to achieve an exceptionally high real-time control over the thickness growth. It turned out that BA and Cu2+ ions significantly impact the film growth process. Reduction of the nanoparticles size and their number was examined via UV-vis spectroscopy and transmission electron microscopy, showing a colossal reduction in the mean diameter of nanoparticles in the case of BA and a moderate reduction in the case of Cu2+. This modification is leading to significant enhancement of the process efficiency through moderation of the topological properties of the films, as revealed by atomic force microscopy. Next, applying infrared, Raman, and X-ray photoelectron spectroscopy, we presented small amounts of metal (B or Cu) in the final structure of PDA and simultaneously their vital role in the oxidation mechanism and cross-linking through covalent or non-covalent bonds. Therefore, we revealed the possibility of synthesizing films via the expected self-assembly mechanism which has hitherto been out of control. Moreover, modification of mechanical properties toward exceptionally elastic films through the BA-assisted synthesis pathway was shown by achieving Young’s modulus value up to 24.1 ± 5.6 and 18.3 ± 6.4 GPa, using nanoindentation and Brillouin light scattering, respectively.