Membrane biofouling remains a critical limitation in wastewater treatment using ultrafiltration (UF) membranes. In this study, polyether sulfone (PES)-based mixed-matrix membranes (MMMs) were engineered by incorporating a novel Ag-doped sepiolite intercalated reduced graphene oxide (Ag-Sep-rGO) nanomaterial. The hybrid additive imparts dual functionalities enhanced antibacterial activity from silver nanoparticles and anti-adhesion characteristics from sepiolite’s fibrous architecture. The resulting membranes exhibited significantly improved hydrophilicity and a ≈4.48-fold increase in pure water flux compared to the pristine PES membrane. Furthermore, they demonstrated excellent antimicrobial performance against both Gram-positive (Staphylococcus aureus) and Gram-negative (E. coli) bacteria, effectively minimizing bacterial attachment and biofilm formation. The nanofiller’s 3D network introduced nanofluidic pathways and improved membrane wettability, promoting higher permeability and better resistance to fouling. The fabricated membranes were further evaluated using bovine serum albumin (BSA) and humic acid as model foulants to assess anti-protein adhesion and natural organic matter (NOM) removal. The nanohybrid membranes demonstrated excellent fouling resistance, with significantly reduced protein adsorption and enhanced rejection efficiency, confirming their potential for long-term operation in wastewater treatment applications. This study highlights the potential of Ag-Sep-rGO as a multifunctional additive for next-generation antifouling membranes, aligning with sustainable water treatment goals by combining advanced material design with superior filtration performance.