Highly structured network polymers are prepared via a molecular layer by layer technique (mLbL) and used as a model system to study aqueous degradation of polymer thin films in real time. Quantitative analysis of the degradation kinetics was enabled by the use of a quartz crystal microbalance (QCM). We conclude that the common metric of halogen, specifically chlorine, exposure (concentration x time) to be an ineffective normalization unit and showed a multistage adsorption process consistent with the established chemical mechanism. Additionally, degradation progression was tracked at multiple points of exposure to determine the effects of chlorination on the chemical and morphological state of the polymer structure with X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), respectively. The formation of known halogenation products were corroborated with XPS through the high resolution spectra. Insight into the heterogeneous nature of the nanostructural degradation was derived from the AFM images. Periodic rinsing was found to release adsorbed chlorine but had negligible benefits on extending the exposure limits of the polyamide film. Fluorinated amine monomer (3,4-difluoroaniline) was incorporated into the surface of the polymer to determine the effect of limiting N-halogenation and the formation of the halogenated ring product. The modified surface layer reduced the rate and magnitude of chlorine adsorption relative to the neat polyamide surface. The QCM technique was shown to be an effective tool for rapid and high fidelity evaluation of molecular degradation and modification strategies to increase device lifetimes.