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The Pearl River Delta with its network system and estuarine bays is unique and one of the most complicated large-scale estuarine systems in China. In this paper, a long-term morphodynamic model is developed to simulate the long-term morphological evolution of the Pearl River Delta. The concepts of long-term model calibration and verification are discussed. The paleo–estuary bay topography formed in the last interglacial period is reconstructed and serves as an initial and boundary condition of this model with time steps of 100 yr. Events of shorter duration are ignored. The driving forces and control factors considered in the long-term delta evolution include representative tides, sediment supply from the Pearl River system, sea-level variation, sediment condensation rates, and neotectonic movement. Deposition rates and total deposition volume are investigated and determined and then used to calibrate the model. Core data with 14C dating at 30 locations are used to verify the model output with satisfactory results. Approximately 1700 collected cores are carefully analyzed to justify the model-simulated evolution processes.

Morphodynamic analysis is conducted to justify and explain the output of the model on delta evolution and deposition modes. The study also provides more temporal and spatial details to the delta development originated from the effects of the morphodynamic structures, such as bidirectional jets and the “men” system. The model confirms that the complicated morphology, e.g., the rocky islands in the shallow estuarine bays, is one of the important factors affecting the long-term evolution of the Pearl River Delta.

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