Seabed groundwater discharge (SGD) is a hidden and critical pathway for the transport of freshwater and nutrients from the coastal zone to the ocean. Currently, the spatiotemporal evolution mechanisms of SGD in highly permeable sandy coastal multi-layer aquifers remain unclear, which significantly limits the accurate quantification of land-sea interaction processes and the assessment of their ecological and environmental impacts. This study focuses on a typical sandy beach at Tieshan Port in Beihai, Guangxi. In response to the unique field phenomenon of year-round freshwater in intertidal wells, continuous in-situ observations of multi-layer groundwater were conducted to obtain high-resolution time-series data on water level, salinity, radon, CO₂, and nutrients in aquifers at different depths. Combined with high-density electrical resistivity (ERT) towed surveys along the coast and perpendicular to the shoreline, we obtained spatial distribution characteristics of the seabed strata and the freshwater-saltwater distribution. The results indicate that approximately 5 km offshore, there exists a confined freshwater discharge channel controlled by seabed topography, where a stable SGD has developed. The freshwater wells located on the beach origin from the shallow unconfined aquifer. The study confirms that the shallow unconfined aquifer and the deep confined aquifer are independent, resulting in a rare multi-layer SGD pattern. This study reveals the multi-aquifer control mechanisms by tides, seasons, and seabed topography on groundwater-seawater interaction processes. Furthermore, a SGD identification technique was developed, combining in-situ long-term monitoring, marine geophysical surveys, and isotopic tracing. Our research can help improve the theory of land-sea interactions in coastal multi-aquifer systems, and provides data support and technical insights for SGD research.