Efficient tertiary effluent desalination is hindered by membrane biofouling, leading to plant downtime, shortened membrane lifespan, heightened energy consumption, and reduced permeability. While the composition of these biofouling layers is studied, little is known about bacterial succession and function. To address this, we used a benchtop reverse osmosis (RO) system to process synthetic tertiary effluent with diluted sludge. System flux monitoring tracked biofouling layer development, and RO biofilm samples were collected at early and mature stages (48, 72, 120 h). Scanning electron microscopy visualized the samples, and their 16S rRNA genes were sequenced. DNA-stable isotope probing with labeled glucose identified growing taxa in early and late biofouling stages (48, 120 h). Over time, biofouling layer biomass increased, with shifts in bacterial diversity and composition. Proteobacteria, notably oligotrophic genera, dominated early stages along with Bacteriodota, while Actinobacteria increased in mature biofilms. Functional changes included a shift from biosynthesis of cellular components like DNA, peptidoglycan, membrane lipids, and antimicrobials, to production of extracellular polysaccharides and reactive oxygen scavenging agents. In conclusion, our research enhances the understanding of biofouling dynamics within tertiary effluent desalination processes, providing insights that could improve biofouling management strategies in RO desalination systems, potentially applicable to larger-scale operations.