In the area where the river enters the sea, due to the weak hydrodynamic strength of the river and the water upstream, the fine suspended matter carried by the river forms a low permeability covering layer on the river bed surface, thus limiting the water-salt interaction between the river and groundwater. The in-depth study on the exchange of water and salt between tidal river flow and groundwater under the influence of low permeability silt layer has important scientific significance and application value for the utilization and protection of coastal groundwater resources. Taking the Dagu River estuary area of Shandong Peninsula as the study area, a site-scale groundwater numerical model is established on the basis of on-site hydrogeological investigation and monitoring. The groundwater salt dynamics characteristics and the fluxes of tidal river-groundwater water and salt exchange under the influence of low permeability silt layer on the river bed surface are studied for the first time. The effect of permeability and thickness change of low permeability layer on tidal river-groundwater exchange process is quantitatively analyzed. The research shows that under different conditions of low permeability layer, the length of the saline wedge increases and the regression rate of the saline wedge decreases at the initial stage, and gradually reaches the minimum value after about 100 days, then the length of the saline wedge suddenly decreases and the regression rate of the saline wedge increases rapidly, and the regression rate gradually becomes stable after about 600 days. In addition, the fluxes of river-groundwater water and salt exchange show periodic changes, and the fluxes of river-groundwater water and salt exchange decrease with the decrease of permeability or the increase of thickness of the low permeability layer.