Abstract: Based on water depth datasets between 1965 and 2016 in the Lingding Bay and the sedimentary data in different years, the evolution patterns of sedimentology and geomorphology of Lingding Bay under the impact of human activities were analyzed. Results show that: (1) Over the past 40 years, the geomorphological boundaries of Lingding Bay have been significantly narrowed, and the overall shoal-trough scheme of the estuary has been compressed and moved eastward. The water surface area has been decreased, while the water volume increased. The geomorphology of the estuary has become narrowed and deepened. (2) In terms of spatial distribution of surface sediment in different years, the grain size of sediment in 1975 and 2003—2004 exhibited a coarse-fine-coarse distribution pattern from north to south, and grain parameters showed a banded distribution. After 2016, the north-south distribution pattern was no longer prominent. Fine sediments were distributed mainly along the western and eastern shoals, while coarse-grained sediments were distributed in the middle shoal in patch, in the dredging pits in the eastern trough, and in the end of the deep trough in outer Lingding Bay. Spatial distribution of grain parameters had shifted from banded to patchy pattern, indicating a transition from a simple to a more complex sedimentary environment. (3) Under the new pattern, three depocenters occurred in the bay: the inner Lingding Bay depocenter in the northern part of the middle shoal, the western shoal depocenter in the south of Qi'ao Island on the western side of the outer Lingding Bay, and the depocenter at the end of the Lingding Channel in the outer Lingding Bay; and they correspond to the scouring and silting schemes in each region. Human activities have significantly influenced the sedimentation and geomorphology of the Lingding Bay over the past 40 years. This study helps to reveal the geomorphological evolution trends of the Lingding Bay and has important practical implications for the integrated management of the Pearl River Delta, as well as the efficient utilization and management of regional water resources.