Export of biospheric organic carbon from land masses to the ocean plays an important role in regulating the global carbon cycle. High-relief islands in the western Pacific are hotspots for such land-to-ocean carbon transport due to frequent floods and active tectonics. Submarine canyon systems serve as a major conduit to convey terrestrial organics into the deep sea, particularly during episodic floods, though the nature of ephemeral sediment transportation through such canyons remains unclear. In this study, we deployed a sediment trap in southwestern Taiwan's Gaoping submarine canyon during summer 2008, during which Typhoon Kalmaegi impacted the study area. We investigated sources of particulate organic carbon and quantified the content of fossil organic carbon (OCf) and biospheric non-fossil carbon (OCnf) during typhoon and non-typhoon periods, based on relations between total organic carbon (TOC), isotopic composition (δ13C, 14C), and nitrogen to carbon ratios (N/C) of newly and previously reported source materials. During typhoons, flooding connected terrestrial rivers to the submarine canyon. Fresh plant debris was not found in the trap except in the hyperpycnal layer, suggesting that only hyperpycnal flow is capable of entraining plant debris, while segregation had occurred during non-hyperpycnal periods. The OCnf components in typhoon flood and trapped samples were likely sourced from aged organics buried in ancient landslides. During non-typhoon periods, the canyon is more connected to the shelf, where waves and tides cause reworking, thus allowing abiotic and biotic processes to generate isotopically uniform and similarly aged OCnf for transport into the canyon. Therefore, extreme events coupled with the submarine canyon system created an efficient method for deep-sea burial of freshly produced organic-rich material. Our results shed light on the ephemeral transport of organics within a submarine canyon system on an active tectonic margin.