Abstract: Understanding erosion-deposition dynamics in coastal bays is crucial for the sustainable development and management of urban estuaries. This study investigates the interannual erosion–deposition dynamics in Shenzhen Bay from 2002 to 2020. Field-measured topographic data alongside empirical orthogonal function (EOF) analysis and quantitative sediment assessment were used to identify the primary factors influencing these patterns. The findings reveal that Shenzhen Bay experiences a general trend of deposition, with the inner and outer bays undergoing an annual sediment accumulation of 675400 m³ (averaging 1.5 cm/a) and 352200 m³ (averaging 0.98 cm/a), respectively. In the inner bay, deposition primarily develops at the boundary between deep channels and shallow flats; however, this pattern gradually declines toward equilibrium as sediments accumulate in the tidal flats. In contrast, the outer bay is characterized by sediment accumulation in deep channel areas. The south channel in the inner bay continues to narrow, shifting from a “wide-narrow” profile to a “uniform-width” profile. This shift is accompanied by the channel apex moving leftward and a downstream extension of the river-dominated area. Tidal currents drive external sediment inputs from Lingdingyang Bay, which represents the principal source of deposition in Shenzhen Bay. The evolution of Shenzhen Bay is primarily shaped by morphodynamic interactions that are dominated by tidal forces, and its erosion-deposition dynamics are significantly influenced by the dynamics of Lingdingyang Bay during extreme weather events. Thus, the management of Shenzhen Bay should be tailored to the erosion-deposition dynamics that are dominated by external sediment inputs and primarily driven by tidal currents.