Abstract: With the growing demand for water reuse, wastewater treatment facilities must effectively manage emerging contaminants and their byproducts to ensure public safety. Excessive use of benzalkonium chloride disinfectants has raised concerns due to the resulting accumulation of benzylamines, such as N-methylbenzylamine (MBA) and N,N-dimethylbenzylamine (DMBA), in wastewater. In response to increasing emphasis on energy efficiency and carbon reduction, biological anaerobic treatment is gaining popularity. This study investigated the biodegradation of MBA and DMBA under anaerobic conditions, their influence on toxic byproduct formation during subsequent chloramination, and their impact on bioreactor performance, degradation pathways, and microbial community structure. Our findings revealed that anaerobic treatment maintained overall performance despite the presence of benzylamines. However, MBA exhibited significant resistance to biodegradation, while DMBA underwent substantial transformation. Chloramination of MBA-treated effluent resulted in nitroso-MBA formation with a 1% molar yield. In contrast, chloramination of DMBA-treated effluent led to notable N-nitrosodimethylamine (NDMA) formation, with molar yields reaching 10 ± 1% and 97 ± 7% of the influent and residual DMBA concentrations, respectively. Microbial community analysis showed distinct differences in the DMBA reactor compared to the MBA and control reactors, supporting proposed degradation pathways and microbial involvement. To further assess environmental relevance, we collected real water samples from a real wastewater treatment plant in southern Taiwan. Our analyses confirmed the presence of these contaminants and their transformation products in the real treatment processes. Interestingly, preliminary results suggest that aerobic biological treatment may be more effective in degrading benzylamines and suppressing nitrosamine formation. Ongoing investigations aim to elucidate the underlying mechanisms behind these observations.