Biofloc technology (BFT) is an eco-friendly aquaculture model that utilizes zero-exchange water. In this study, we investigated the integration of duckweed into BFT in an effort to enhance nitrogen, phosphorus, and carbon utilization and to improve animal welfare for cultivating Megalobrama amblycephala. The experiment spanned 75 days, comparing a group of M. amblycephala supplemented with duckweed (DM) to a control group (CG) with no supplementation, where duckweed consumption relied solely on the feeding behavior of the fish. The concentrations of nitrate, total nitrogen, and phosphorus accumulation were lower in the DM than in the CG from day 45 onwards, with differences of 16.19, 26.90, and 1.45 mg/L, respectively, at the end of the experiment. The DM showed simultaneous increases of 5.77, 11.20, and 5.07 % in the absolute utilization of nitrogen, phosphorus, and carbon, respectively. The abundance of TM7a (10.27 %), linked to nitrate absorption, became the dominant genus in the water of the DM. Additionally, the abundance of Cetobacterium, associated with carbohydrate digestion, was significantly higher in gut of the DM (23.83 %) than in the gut of CG (1.24 %, P < 0.05). Supplementing the diet of M. amblycephala with duckweed improved digestion and antioxidant enzyme activity. Transcriptome data showed that duckweed supplementation resulted in an increase in the expression of genes related to protein digestion and absorption and carbohydrate metabolism in M. amblycephala, and analysis of the significantly enriched pathways further supported improved antioxidant capacity. Based on the above results, we concluded that as M. amblycephala consumes more duckweed, the differences in nitrogen and phosphorus levels between the DM and CG would continue to increase, along with a simultaneous increase in fixed carbon. Thus, this study achieved the goal of recycling BFT resources and improving animal welfare by integrating duckweed.