In order to explore the response of estuarine salt intrusion to river and tidal forcing as well as water depth under the influence of human activities and climatic changes, a three-dimensional numerical salinity model for three-dimensional ideal estuaries was established. By analyzing the vertical and lateral distributions of longitudinal circulation and salinity, the effects of vertical salt transport induced by the vertical and lateral shear as well as the tidal pumping on saline intrusion, and the response of salt transport to radial tidal dynamics and water depth were studied. The results show that the salt intrusion is sensitive to changes in the river runoff and tidal forcing. In a relatively deep estuary, increasing the runoff or tidal forcing can reduce salt intrusion throughout the estuary. In shallower estuaries, the increase of tidal drive causes the opposite trend of tidal-averaged salinity change in the upstream and downstream of the estuary, which can be explained by the response of longitudinal salt transport to radial tide depth conditions caused by transverse shear, longitudinal shear and tidal pump respectively.