The uncertainty and sensitivity of predicted positions and thicknesses of seawater-freshwater mixing zones with respect to uncertainties of saturated hydraulic conductivity, porosity, molecular diffusivity, longitudinal and transverse dispersivities were investigated in both head-control and flux-control inland boundary systems. It shows that uncertainties and sensitivities of predicted results vary in different boundary systems. With the same designed matrix of uncertain factors in simulation experiments, the variance of predicted positions and thickness in the flux-control system is much larger than that predicted in the head-control system. In a head-control system, the most sensitive factors for the predicted position of the mixing zone are inland freshwater head and transverse dispersivity. However, the predicted position of the mixing zone is more sensitive to saturated hydraulic conductivity in a flux-control system. In a head-control system, the most sensitive factors for the predicted thickness of the mixing zone include transverse dispersivity, molecular diffusivity, porosity, and longitudinal dispersivity, but the predicted thickness is more sensitive to the saturated hydraulic conductivity in a flux-control system. These findings improve our understandings for the development of seawater?freshwater mixing zone during seawater intrusion processes, and give technical support for groundwater resource management in coastal aquifers. The uncertainty and sensitivity of proposed positions and thicknesses of seawater-freshwater mixing zones with respect to uncertainties of saturated hydraulic conductivity, porosity, molecular diffusivity, longitudinal and transverse dispersivities were investigated in both head-control and flux-control inland boundary systems. that uncertainties and sensitivities of predicted results vary in different boundary systems. With the same designed matrix of uncertain factors in simulation experiments, the variance of predicted ations and thickness in the flux-control system is much more than that predicted in the head-control system In a head-control system, the most sensitive factors for the predicted position of the mixing zone are inland freshwater head and transverse dispersivity. However, the predicted position of the mixing zone is more sensitive to saturated hydraulic conductivity in a flux-control system In a head-control system, the most sensitive factors for the p redicted thickness of the mixing zone include transverse dispersivity, molecular diffusivity, porosity, and longitudinal dispersivity, but the predicted thickness is more sensitive to the saturated hydraulic conductivity in a flux-control system. these findings improve our understandings for the development of seawater? freshwater mixing zone during seawater intrusion processes, and give technical support for groundwater resource management in coastal aquifers.