Impounding by the Three Gorges Project (TGP) changed the hydrological process and affected the ecosystem in the middle and lower reaches of the Yangtze River. Poyang Lake is closely linked with the Yangtze River. This paper presents a coupled numerical model designed for simulating the tempo-spatial variation of water quantity and quality in the lake’s water system that features complex river-lake interactions. According to the calculated results of a typical year (2000) under two scenario schemes, we evaluated TGP’s effects on the ecological environment of the lake. The results show that due to TGP impoundment, the hydraulic gradient at the lake outlet has increased and that the outflow fluctuates dynamically and regularly with the increase and decrease of the TGP released discharge. The lake water level falls in advance and the average reduction magnitude of the water level decreases progressively from north to south, showing a spatially uneven effect, which is 0.95 m, 0.70 m, 0.74 m, 0.35 m, and 0.80 m at Xingzi, Tangyin, Duchang, Kangshan, and Wucheng stations, respectively. The ammonia nitrogen output from the lake to the Yangtze River increases and the total ammonia nitrogen amount within the lake region decreases. The average ammonia nitrogen concentration within the lake region tends to increase slightly and the influence magnitude on the concentration is reduced from north to south. The wetland vegetation area fluctuates dynamically with the decline of the water level, and the increase of the wetland vegetation area ranges from 0.64 to 215.48 km². As a result of the falling water levels, the bottomlands in the lake region are exposed relatively earlier and the continuous exposure days increase, which intensifies the problem that migrant birds do not have enough food. Meanwhile the number of days when the bottomland and wetland are submerged decrease, which will further accelerate the degradation succession of wetland vegetation.