To address the inadequate removal of antibiotic resistance genes in wastewater treatment plants, this study investigated the impact of bioaugmentation with dried Eichhornia crassipes roots on removal of antibiotics sulfamethoxazole, tetracycline and erythromycin from pharmaceutical wastewater while optimizing potential for reclaiming value through biogas production, utilizing an anaerobic membrane bioreactor (AnMBR). Three sets of AnMBRs were set up for the experiment, C1 (inoculum), C2 (inoculum + antibiotics) and EC (inoculum + antibiotics + E. crassipes). The results showed that E. crassipes mitigated some of the toxic effects of antibiotics on the microbial community and prevented negative impact on the archaeal community, and significantly increased average biogas production (by 37% compared to control without antibiotics and 42% compared to control with antibiotics) as well as antibiotics removal. Furthermore, bioaugmented reactor showed significant reduction of erythromycin (97%) and tetracycline (83%) concentrations in effluent. Utilization of E. crassipes root offers a simple yet powerful tool for preventing the emergence of antimicrobial resistance and dissemination of such pollutants into the environment.