In this study, we analyzed the clay mineralogy and geochemistry of surface and drill core samples from the northeastern Beibu Gulf in order to unravel the sediment provenance of, and factors controlling, the sedimentary environment. The main clay mineral assemblage in the surface sediment samples included kaolinite (27–72%), smectite (4–51%), illite (7–20%), and chlorite (8–17%). The study area comprises three major clay distribution zones (from the northeastern coastal area to central Beibu Gulf basin), i.e., the kaolinite-dominated, kaolinite–smectite, and smectite-dominated zones. The zoning of the clay mineralogy and major and trace elements indicated the mixing of coarse terrigenous sediments with distal fine sediments. Early Holocene sea level rise was documented in core B15-1, which had three sedimentary units (divided into Units 1–3 from top to bottom), as revealed by the changes in the dominant clay minerals and geochemical/oxide ratios (SiO2/Al2O3, Rb/Sr, Sr/Ba, and Ti/Ca) in Unit 2. Unit 1 and Unit 3 were likely deposited in the continental and marine environments, respectively. The low sedimentation rate and hydrodynamic disturbance may have influenced the deposition process more than climatic fluctuations.