Although there are several rivers that flow through the Iya Valley region, the Iya River (祖谷川 "Iya-gawa") is the principal one, flowing from east to west and forming the entirety of the Iya Valley. Mount Tsurugi (剣山 "Tsurugi-san"), the second-highest peak on Shikoku island, is at the east end of the Iya Valley along the border with Tsurugi town, and from here the headwaters of the Iya River begin their flow from springs that come off the mountain, some of which are as high as 1800m. The Iya Valley follows this river for about 50 km, to the village of Iyaguchi (祖谷口) in Yamashiro District of Miyoshi City, where the Iya River joins the Yoshino River at an elevation of about 90m.