The Fangliao submarine canyon cuts across the shelf and slope of southwest Taiwan. Unlike other canyons along this margin, there is no obvious connection to an individual fluvial sediment source on land. Two recent cruises to Fangliao Canyon provide insight into sedimentation associated with a major typhoon. Box and piston cores were retrieved from Fangliao Canyon in early January 2007, after a local earthquake and an extended period of low-to-moderate river flow in streams that are suspected of contributing sediment to the canyon. Similar cores were collected from the canyon in early October 2009, following one of the largest typhoons to hit Taiwan in the past several decades. Typhoon Morakot delivered several meters of rain to Taiwan, with the largest river floods occurring in the south and southwest regions. In addition, the coastal ocean environment was energized by significant wave heights (>12m). Comparisons of textural, radioisotopic, and geochemical data reveal likely sediment transport and depositional processes within and surrounding Fangliao Canyon. Typhoon Morakot caused a layer ~10cm thick (and greater) throughout the canyon. X-radiographs of the 2007 cores show limited physical structure in most cases, and the 2009 radiographs display obvious changes in sediment density relative to the underlying sediment, as well as distinct physical lamination. Examining signals from different geochemical and radiochemical tracers for terrestrial sediment source indicates that the flood layer deposited by Typhoon Morakot came from several small mountainous rivers. By comparing the results of the 2007 cruise with those from 2009, we gain significant insight to the close linkage between a line source of fluvial sediment and deposition in a submarine canyon, as well as the role that tropical-storm events can play in delivering sediment to these environments.