Many estuaries have been damaged by such material movements as marine debris, suspended sediment, and pollutants. Understanding the estuarine circulation system is necessary to solve such problems. Salt transport analysis provides an insight into hydrodynamic processes about material circulation in the estuary. In this study, to understand the mechanisms of salt transport, a three-dimensional hydrodynamic model was applied in the hypertidal estuary system—Yeomha Channel in Gyeonggi Bay. The simulation period of the model was a total of 245 days (20 January to 20 September 2020), including the dry and wet seasons. The model results for the temporal variation in tide, current velocity, and salinity were validated by comparing them with the observed in-situ data. The total salt transport (FS) was calculated in three cross sections of the Yeomha Channel and was decomposed into three components (QfS0: advective salt transport; FE: steady shear dispersion; FT: tidal oscillatory salt transport). During the dry season with strong tidal forces, the total salt transport patterns were mainly dominated by QfS0. During the wet season with high river discharge, the total salt transport patterns were determined by the balance between QfS0, FE, and FT. The long-term tidal constituents (MSf and Mm) were the main mechanisms causing QfS0 with the spring–neap variation during the dry season. The tidal trapping effect, caused by a phase difference of less than 90° between tidal current and salinity, generated landward FT in the dry and wet seasons. In addition, the high river discharge during the wet season decreased the phase difference between tidal current and salinity to less than 70 °, resulting in a much stronger landward FT. This study suggests that the long-term tidal constituents and tidal trapping effect are unique characteristics that contribute to material circulation in the hypertidal estuary.