The rapid expansion of urban areas and the increasing demand for water resources necessitate substantial investments in technologies that enable the reuse of municipal wastewater for various purposes. Nonetheless, numerous challenges remain, particularly regarding disinfection by-products (DBPs), especially carcinogenic compounds such as N-nitrosamines (NTRs). To tackle the ongoing issues associated with reverse osmosis (RO) membranes, this study investigated the rejection of NTRs across a range of commercially available RO membranes. In addition, the research aimed to improve rejection rates by integrating molecular plugs into the nanopores of the polyamide (PA) layer. Hexylamine (HEX) and hexamethylenediamine (HDMA), both linear chain amines, have proven to be effective as molecular plugs for enhancing the removal of NTRs. Given the environmental and human health concerns associated with linear amines, the study also aimed to assess the feasibility of diamine molecules as potential alternatives. The application of molecular plugs led to changes in pore size distribution (PSD) and effective pore number, resulting in a decrease in membrane permeability (from 5 to 33%), while maintaining levels suitable for RO processes. HEX and HDMA exhibited a positive effect on NTR rejection with ACM1, ACM5 and BW30LE membranes. In particular, NDMA rejection, the smallest molecule of the tested NTRs, with ACM1 was improved by 65.5% and 70.6% after treatment with HEX and HDMA, respectively.