It rises in the Central Oregon Coast Range in western Lane County, approximately 10 mi (16 km) west of Veneta. It flows east through the mountains to Veneta, through the Fern Ridge Reservoir, and then north into the Willamette Valley, roughly parallel to and west of the Willamette River. It joins the Willamette from the southwest approximately 10 mi (16 km) south of Corvallis.
The watershed includes approximately 410 sq mi of land (262,000 acres, 1060 km²) zoned as 45% forest, 30% agricultural, 8% public, and 17% urban or rural residential. The Long Tom waters support more than 140,000 people in the area, including residents in the city of Veneta and the rural farming communities of Alvadore, Cheshire, Crow, Franklin, and Noti, as well as industrial and commercial land on the western edge of Eugene. These lands were inhabited by the Chelamela group of the Kalapuya Indians prior to European settlement.
The Oregon Country Fair works actively with the Long Tom Watershed Council to restore the portion of the Long Tom that passes through the fair site.