The estuary area of the Zhujiang River Delta is significantly influenced by its drainage and offshore environment. Since being under the interaction of sea and land, the depositional system within the estuary area could be of great potential to reveal the simultaneous succession of geological and geomorphic processes. This paper presents a magnetic investigation report of a sedimentary core drilled from the Lingdingyang Bay at the Zhujiang River Estuary. Results of this study show that, the concentration of magnetic minerals or the source area of the high-coercivity magnetic minerals within the core sediments is relatively constant during the two periods of relatively high sea-level (i.e., under marine transgression) since late Pleistocene, revealing a stable sedimentation environment or a relatively fixed sediment source, respectively; however, during the period of marine regression, when the weathering and denudation processes dominate, the magnetic mineral composition in sediments is characterized by significant large-scale fluctuations, possibly indicating that the source areas of detrital materials have undergone a dramatic climate evolution. Multiple environmental magnetic parameters, including low-frequency magnetic susceptibility, anhysterestic remanent magnetization, saturation isothermal remanent magnetization, and HIRM (the ‘hard’ isothermal remanent magnetization), reveal a synchronous pattern of magnetic variations through the core. In comparison, the S-ratio record of the core sediments is more sensitive to the sedimentation evolution history during the marine transgression and regression in the Lingdingyang Bay at the Zhujiang River Estuary.