Abstract: The subterranean estuary (STE) serves as a critical interface for land-sea material exchange and biogeochemical transformations in coastal zones, playing an important regulatory role in coastal phosphorus (P) cycling. This study investigated a sandy coastal STE in Beihai, Guangxi, by establishing a land‒sea transect and systematically collecting groundwater and sediment samples at different depths during a tidal cycle. Combined with in situ hydrological monitoring and multi-parameter geochemical analysis, the study revealed the pathways and controlling mechanisms of phosphorus migration. The results demonstrate that the study area can be divided into three functional units: the upper landward zone, the upper saline plume (USP) zone, and the seaward zone. Each zone exhibits distinct phosphorus cycling characteristics. Dissolved phosphorus in groundwater showed a spatial distribution pattern of “higher in the mixing zone and lower at both ends”, with significantly elevated concentrations in the USP zone during flood tide. Phosphorus cycling was co-regulated by multiple processes: the adsorption–reductive dissolution of iron oxides dominated in the USP zone, while competitive adsorption by dissolved silicon, calcium salt precipitation, and organic matter decomposition jointly influenced phosphorus behavior in the seaward zone. Nutrient structure analysis further indicates a widespread high N/P ratio in the region, with phosphorus as a potential limiting factor that may exacerbate ecological structural imbalance and eutrophication risk in coastal waters. This study elucidates the key pathways and driving mechanisms of phosphorus cycling in sandy coastal STEs and provides a scientific basis for water quality management and ecological risk prevention in the Beibu Gulf.