The evolution of the Pearl River Estuary (PRE) in China has been intensely disturbed by diverse human activities in recent decades. In this study, the morphological changes of Lingding Bay in the PRE, consisting of three shoals (West, Middle, and East Shoals) and two channels (West and East Channels), in response to human activities since the 1970s were examined. From 1974 to 1985, the subaqueous delta was dominated by siltation, with siltation in the West and Middle Shoals but erosion in the East Shoal and West Channel. From 1985 to 1999, the subaqueous delta was eroded with increasing water volume of 347.9 × 106 m3, resulting from the combined influences of land reclamation and channel dredging. In addition, water area in the Lingding Bay reduced by 8.0% in 1999 compared with that in 1985. From 1999 to 2011, the water area continued to decrease and water volume still increased, indicating the subaqueous delta was narrowed and deepened. And the Middle Shoal was dominated by siltation, but other geomorphic units were eroded. Furthermore, the subaqueous delta in inner and outer Lingding Bay switched from siltation to erosion and from erosion to siltation during this period compared with the previous period of 1985–1999, respectively. Such phenomenon revealed that the sediment sink had evolved towards outer Lingding Bay (i.e., southern subaqueous delta) during this period. Our study has important implications for understanding the individual and combined effects of human activities on the evolution mode of PRE and provides scientific guidelines for the sustainable managements in the PRE.