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Conventional municipal wastewater treatment plants (WWTPs) receive a range of trace organic chemicals like pharmaceuticals and personal care products (PPCPs), and pest control chemicals (PCCs), but are not specifically designed to remove them. Due to health and ecological concerns, advanced treatments such as nanofiltration (NF) are considered. However, conventional pressurized NF requires expensive pretreatment and high-pressure. The novel submerged NF (SNF) offers a promising alternative avoiding these issues, but removal efficiency and managing the PPCP and PCC-rich concentrate need investigation. This study assessed SNF using NF270 membranes with molecular weight cut-off (MWCO) of 360 Da and ESNA5 membranes with MWCO of 295 Da to remove PPCPs and PCCs and treat concentrate via anaerobic digestion. Results showed SNF operated continuously for up to 38 days in dead-end and feed-and-bleed modes at 75% recovery. NF270 achieved a flux of 2.0 L/m 2 h with 40–74 kPa transmembrane pressure (TMP), while ESNA5 required a lower flux of 1.5 L/m 2 h and higher TMPs of 72–95 kPa due to higher salt rejection. Observing 21 selected PPCPs and PCCs, ESNA5 demonstrating the best removal (60–98%) attributed to its lower MWCO. Size exclusion was the primary separation mechanism. Dead-end mode showed lower fouling, and ESNA5 foulants showed higher in inorganic content. Anaerobic digestion of NF270 concentrate degraded some chemicals, but recalcitrant ones (e.g., carbamazepine, lamotrigine, desvenlafaxine, tramadol, venlafaxine, fexofenadine) persisted and accumulated in the biosolids. In summary, SNF effectively reduced PPCPs and PCCs in wastewater, warranting scaled-up trials and potential application in recycled water schemes. • Submerged nanofiltration reduced trace organic chemicals in treated wastewater. • Two nanofiltration membranes were evaluated in dead-end and feed-and-bleed modes. • Stable operation over 38 days can be achieved without membrane cleaning. • Rejection of 80 detected trace organic chemicals, mainly driven by size exclusion. • Anaerobic digestion of concentrate partly shifted trace chemicals into biosolids.