Lake eutrophication has become a global environmental problem and severely affects water resource quality. Although studies have addressed eutrophication, the mechanisms are not fully understood to date because of the water-biomass-sediment complexity in lakes, and limited observation data makes analysis of the entire nutrient evolution process difficult. Therefore, to reveal eutrophication mechanisms more comprehensively, analysis should be based on long-term processes of nutrient changes. In lake ecosystems, all stresses and forces interact during the eutrophication, among which, hydrology and ecosystem play key roles. Hydraulic residence time impacted nutrient supply, lake productivity, and nutrient accumulation processes profoundly. With water cycles and energy exchanges in lake ecosystems, primary productivity is a critical process contributing to lake trophic states. Poyang Lake, the largest fresh water lake in China, is located on the southern bank of the middle-reach of the Yangtze River. Compared with most other eutrophic lakes in the region, water quality of Poyang Lake was mesotrophic during the 20th century. However, water quality has declined since the beginning of the 21th century. To discern the trophic evolution of Poyang Lake, hydraulic residence time and lake ecosystem-nutrient dynamic models, were used in the present study to determine long-term changes of nutrients and biomass in the lake. Furthermore, sediment records, including total organic carbon(TOC), Pollen concentration and DI-TP series derived by using diatom-TP transfer function, compared the simulation results of the past 300 years. The simulation revealed that nutrient TP changed differentially in response to changes in climatic-hydrological and climatic-ecosystem conditions. Control runs for 1955-2008 proved that TP increase was consistent with the observed growth of primary producer biomass. On this basis, we ran the models for a long-term period from 1700 to 1899. The time-series analysis for the simulations showed that the period 1812-1828 was synchronized between hydrology-forced and ecosystem-feedback nutrient changes. Ratio of hydrology and aquatic biomass accounted for 79.1% and 20.9% of this simulated annual series. The period 1844-1860 AD showed an asynchronous match in which hydrology-forced and ecosystem-feedback nutrient changes occurred. The ratio of the two were 36.4% and 63.6%, respectively. In the simulated time series, the synchronous period was 62.5% of the entire time, suggesting climatic-hydrological factors played a major role in the process of nutrient evolution. Although the asynchronous period only accounted for 12.5%, it also had a critical effect on TP changes in the lake. Furthermore, simulations of nutrient and biomass were done by correlation analysis. The result revealed a quasilinear relationship between nutrient TP and biomass. However, a bifurcation appeared when TP > 40%, indicating a threshold existed in this pattern, suggesting that TP changed significantly differently when it increased above the threshold and decreased below the threshold.