Abstract: Establishing lake nutrient reference conditions scientifically and reasonably is one of essential technical foundations for nutrient criteria determination. A system dynamics-based method, combined with several mathematical models, was undertaken to simulate the nutrient sources, distribution and movement in Lake Qionghai, Sichuan Province. The evolution process of nutrient concentrations and eutrophication levels in the past decades under different hydrological conditions was modeled by a system retrieval method. The results showed that the system simulation model calibrated by experiments was capable of describing the historical changes of lake eutrophication. Accordingly, this new method identified the reference total phosphorus values of 0.008-0.015 mg/L, reference total nitrogen values of 0.286-0.323 mg/L, reference chlorophyll-a values of 2.140-4.211 μg/L, and reference Secci depth values of 1.862-2.731 m for Lake Qionghai.