A tsunami generated by the C.E. 1707 Hōei earthquake is largely thought to be the flood event of record for southwestern Japan, yet historical documentation of the event is scarce. This is particularly true in northwestern Shikoku within the Bungo Channel, where significant inconsistencies exist between historical records and model-derived tsunami heights. To independently assess flooding from the C.E. 1707 Hōei tsunami in the context of the region’s long-term flooding history, we present complementary reconstructions of extreme coastal inundation from three back-barrier lakes in the northern Bungo Channel: Lake Ryuuoo, Lake Amida, and Lake Kamega. At all sites, the most prominent marine overwash deposit of the past ~1,000 years, as defined by grain size, density, and geochemical indicators, is consistent with the timing of the 1707 tsunami, providing strong evidence that the event caused the most significant flooding of the last millennium in this region. At Lake Ryuuoo, modern barrier beach elevations and grain sizes in the tsunami’s resultant deposit provide ~4 m as the first physically based height constraint for the 1707 tsunami in the northern Bungo Channel. Around 1,000 years ago, a concurrent and abrupt transition in lithology observed at all three sites is also consistent with rapid, regional geomorphic change. At Lake Ryuuoo, a marine overwash deposit comparable to the 1707 deposit directly overlies this transition. A 1,000-year-old lithological transition or deposit has not been observed at sites closer to the mouth of the Bungo Channel, suggesting that the deposit in Lake Ryuuoo is more consistent with a tsunami generated by local seismicity along the Japan Median Tectonic Line than with a Nankai Trough-derived tsunami. Our findings are significant in that they provide three new millennial-scale tsunami inundation reconstructions for a relatively understudied region of Japan, along with the first physically based height constraint for the Hōei tsunami in the northern Bungo Channel.