Reverse osmosis (RO), an important membrane technology for producing process and tap water, faces challenges due to biofilms formed by viable microorganisms, which significantly impair membrane performance. Disinfection is commonly employed to suppress biofilm formation but can also damage the crucial selective upper layer of the membrane. The present study aims to improve and compare analytical methods for detecting membrane damage to aid the design of targeted disinfection approaches that do not compromise RO efficiency. To achieve this, the accompanying byproducts of in-situ formed chlorine dioxide are analyzed individually with regards to their harmfulness for RO membranes. Combined insights from ATR-FTIR investigations, the methylene blue (MB) dye test, and XPS measurements enable a systematic assessment of the chemical constituents in the chlorine dioxide, ranking their harmfulness as: chlorite < persulfate < purified chlorine dioxide < free chlorine. Further investigations reveal that mechanical stress in the form during disinfection significantly accelerates membrane damage during disinfection. The results of this study pave the way for improved RO processes that account for the effects of chemical byproducts and mechanical stresses to balance disinfection efficacy and membrane integrity for environmentally sustainable water purification solutions.