An experiment was conducted to determine the growth efficiency of lotus (Nelumbo nucifera Gaertn) on nutrient capture in farming systems of yellow catfish (Pelteobagrus fulvidraco Richardson). Three treatments, a control treatment of N. nucifera alone (T1), a treatment of N. nucifera-P. fulvidraco co-culture (T2) and a treatment of P. fulvidraco alone (T3), were conducted in triplicate. Except pH, conductivity and chemical oxygen demand (CODMn), most of the water quality parameters were significantly lowered by N. nucifera cultivation. Total nitrogen and phosphorus concentrations in the T2 system were 62.2% and 71.6% higher than those in the T1 system respectively; and 31.8% and 59.2% lower than those in the T3 system respectively. The nitrogen and phosphorus release rates were 41.2% and 36.8% in the T2 system, respectively, and 95.6% and 99.1% in the T3 system respectively. 7.31%-21.4% of nitrogen and 3.35%-15.9% of phosphorus were unaccounted. N. nucifera can effectively remove nutrients from water and sediments and may promote the outflow of nutrients. No significant difference in fish or N. nucifera growth performance was observed among the systems. This study indicates that the co-culture of N. nucifera with P. fulvidraco is an optimal culture system that can increase food production and reduce waste discharge.