The impact of water hyacinth (Eichhornia crassipes) root biomass (WHRB) on pharmaceutical wastewater treatment with an aerobic hollow-fiber membrane bioreactor (HF-MBR) was investigated. The performance of the bioreactor was assessed in terms of COD (Chemical Oxygen Demand) and antibiotic removal and membrane biofouling rate. For deeper insight, microbial communities in sludge and biofilm layers were analyzed through Illumina sequencing. The addition of WHRB into the HF-MBR increased the COD (by 6%), as well as antibiotics and transformation products removal efficiency. Removal efficiencies of 97%, 98% and 84% were obtained for removal of erythromycin, sulfamethoxazole, and tetracycline. Furthermore, WHRB modified the biodegradation network, increased the relative abundances of Chloroflexi, Proteobacteria and Nitrospirae and decreased Firmicutes, compared with the control with antibiotics. The addition of WHRB also enriched Actinobacteria and Bacteroidetes while decreasing the phylla Chloroflexi and Saccharibacteria in the biofilm.