Estuary morphology changes significantly with intensive human intervention, resulting in dynamic structural variations in the estuary. However, little is known about the threshold sizes of estuary morphology that ensure water security. A two-dimensional width-averaged semi-analytical model is applied to explore the impacts of human-induced alterations in bathymetry and geometry on tidal and salt dynamics in Lingdingyang Bay (LDYB). Salt flux (Fs) is positively correlated with tidal flux (Ft) and negatively correlated with tidal energy flux (Fte). Greater geometric convergence reduces Ft and increase Fte. Increased water depth increases Ft and Fte. Thus, both greater geometric convergence and increased bathymetry enhance tidal hydrodynamics. Saltwater transport is weakened by greater geometric convergence and enhanced by increasing water depth. Sensitivity experiments are conducted using maximum water level and salt intrusion length as the criterion. Thresholds for morphological sizes in the LDYB are found to be a convergence ratio (convergence length over mouth width,LcB0) of 0.83–0.88 and a combined depth factor (α) of 1.04–1.07. Moreover, transition of the estuarine morphology from an exponential convergent shape to a prismatic shape had a limited effect on tidal hydrodynamics when the convergent length rate (e-folding convergence length over total convergence length,LeLc) is >0.61. These results notice that human activities, such as reclamation and tidal channel dredging, exacerbate the risk of salt intrusion and should be applied with caution.