Global activities of typhoons and hurricanes are gradually changing, and these storms can drastically affect lake ecosystems through the recession of submerged macrophytes that regulate the water quality in lakes. Using an echosounder, we captured the short-term, massive loss of submerged macrophytes attributed to the abnormal fluctuation of the water level induced by the approach of a catastrophic super typhoon in the south basin of Lake Biwa, Japan. This paper investigates the physical processes responsible for the loss of vegetation using a high-resolution circulation model in Lake Biwa as a pilot study area. The circulation model was coupled with dynamical models of the fluid force and erosion acting on the vegetation. Our simulation successfully reproduced the water level fluctuation and high-speed current (torrent) generated by the typhoon gale. The simulated results demonstrate that the fluid force driven by the gale-induced torrent uprooted submerged macrophytes during the typhoon approach and that this fluid force (rather than erosion) caused the outflow of vegetation. As a result, this uprooting attributed to the fluid force induced the massive loss of submerged macrophytes in a large area of the south basin, which might have increased primary production and reduced the stock of fish such as bluegill in the lake. Our approach is practical for evaluating changes in lake environments attributed to the massive outflow of submerged macrophytes under various climate change scenarios. (227 words)