Abstract: The nitrogen and phosphorus loadings into the lake are divided into two parts: point sources and non-point sources. The Soil Conservation Service (SCS) model and Universal Soil Loss Equation (USLE) model were respectively employed to estimate the non-point source loadings of dissolved nitrogen and phosphorus into the lake. The point source loadings of nitrogen and phosphorus were estimated according to the discharge of lakeside domestic and livestock wastewater. The nutrient loadings out of the lake were calculated on the basis of rivers out of the lake, water intake and fishing in the lake. With this calculated loadings out of and into the lake and the currently available data on total nitrogen and total phosphorus concentrations of in the lake, and based on the principle of mass conservation of total nitrogen and total phosphorus, the net sedimentation velocity of total nitrogen and total phosphorus was calculated. Then, the previous annual average concentrations of total nitrogen and total phosphorus in the lake could be obtained by backward inference, and the reference conditions for total nitrogen and total phosphorus could be established. Based on the proposed model, the reference conditions for total nitrogen and total phosphorus in Lake Qionghai were 0.018 and 0.239 mg/L, respectively. The proposed reference conditions inference model required less data with clear physical concept. Thus, the proposed approach could be used in other lakes lacking sufficient data.