The worldwide prevalence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have become one of the most urgent issues for public health. Thus, it is critical to explore more sustainable methods with less toxicity for the long-term removal of both ARB and ARGs. In this study, we fabricated a novel material by encapsulating zinc oxide (ZnO) nanoflowers and activated carbon (AC) in an alginate biopolymer. When the dosage of ZnO was 1.0 g (≈2 g/L), the composite beads exhibited higher removal efficiency and a slight release of Zn2+in water treatment. Fixed bed column experiments demonstrated that ZnO/AC alginate beads had excellent removal capacities. When the flow rate was 1 mL/min, and the initial concentration was 107CFU/mL, the removal efficiency of ARB was 5.69-log, and the absolute abundance of ARGs was decreased by 2.44–2.74-log. Moreover, the mechanism demonstrated that ZnO significantly caused cell lysis, cytoplasmic leakage, and the increase of reactive oxygen species induced subsequent oxidative stress state. These findings suggested that ZnO/AC alginate beads can be a promising material for removing ARB and ARGs from wastewater with eco-friendly and sustainable properties.