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As the largest hydropower project in China, the impact of the Three Gorges Project (TGP) on the ecological environment has aroused public attention and has been studied from various aspects. After the TGP was operated, seasonably adjusted runof f by the Three Gorge Reservoir (TGR) might cause great changes of hydrological regime in the lower reaches of the Yangtze River, especially the estuarine areas where seawater intrusion is strong and salt-water environment is complicated. The salt-water dynamics in this region will be greatly influenced in response to the operation of TGP. In order to study the impact of the project on salt -water dynamics and soil salinity, a field experiment has been carried out in the Yangtze River Estuary (YRE). This paper seeks to investigate the influence of the TGR on salt-water dynamics and soil salinity in YRE through the analysis of the relationship between the impact factors of salt - water dynamics in the estuary area. Results showed that the estuarine runoff was closely related to the impoundment process, and the estuarine runoff was one of the most important factors that influenced salinity dynamics of water and soil in the estuary. Results showed that discharge of the TGR was affected by its water storage speed, and runoff at Datong station in the estuary was significantly correlated with the reservoir discharge. The reservoir discharge affected Datong runoff and the lag time of influence of the TGR on Datong discharge is about 8 to 9 days. Runoff at Datong station influenced the river water level in the estuary, and impact of the river runoff on the river water level was delayed around 13 days. The lag time of the influence of the impoundment process of the TGR on the estuarine water level is about 20 days. The discharge decrease of the reservoir reached 3600 m3/s during the impoundment period in 2011, and it would cause about 3500 m3/s flow decline at Datong station with 8 days lag. It will result in 15.6 cm drop in the water level and 4.26 mS/cm increase in river water electrical conductivity (EC) in the estuary, which indicated the increase risk of seawater intrusion intensity in the estuary. Significantly positive correlation between river water salinity and ground-water salinity was also observed, and influence of the river water salinity on groundwater salinity increased gradually from the river bank to the inland. Significant correlation existed between groundwater salinity and soil salinity in different soil layers, with the closest relation in the deep layers. Monitoring results showed that salinity of river water, groundwater and soil under impoundment process performed higher than that of non-impoundment process, and it could be inferred that the impoundment process has a certain impact on the salt-water dynamics and soil salinity in the estuary. In summary, soil and groundwater salinity were affected by the TGR, and risk of soil salinization increased.