Five water system connectivity schemes were designed to quantitatively evaluate the connectivity of the western polder area of Gaochun District in Nanjing. Based on the hydrological, hydrodynamic, and water quality models, the water environmental response characteristics under each scheme were simulated. The results show that connecting river channels (scheme 1) significantly improved the water quality of rivers such as the Caotang Xishan River, with annual average mass concentrations of ammonia nitrogen, total phosphorus and total nitrogen in the Caotang Xishan River decreasing by 0.65, 0.14, and 1.21 mg/L, respectively, indicating that river channel connection can accelerate pollutant attenuation. Connecting the Chenglonggang River and Guanxi River (scheme 2) reduced annual average mass concentrations of ammonia nitrogen, total phosphorus, and total nitrogen in the Chenglonggang River by 0.84, 0.15, and 0.90 mg/L, respectively. However, it caused a slight decline in the water quality of Gucheng Lake and rivers such as the Hengxi River, indicating that when the self-purification capacity of the water body is exceeded, the channel connection will pollute originally good-quality water bodies. Deepening river channels (scheme 3) and widening river channels (scheme 4) have a weak impact on the water environment. Increasing tributaries (scheme 5) reduced the water volume of the Qiqiao River, leading to increases in annual average mass concentrations of ammonia nitrogen, total phosphorus and total nitrogen by 0.11, 0.02, and 0.04 mg/L, respectively, thereby negatively affecting the water environment of the lake area of Gucheng Lake downstream.