The Hoodoo River's watershed covers 128 km2 (49 sq mi),[6] and its mean annual discharge is an estimated 8.82 m3/s (311 cu ft/s).

[6] The mouth of the Hoodoo River is located about 68 km (42 mi) east-northeast of Wrangell, Alaska, about 120 km (75 mi) northwest of Stewart, British Columbia, and about 134 km (83 mi) south of Telegraph Creek, British Columbia.

[12] The Hoodoo River originates from the meltwaters of Hoodoo Glacier, a valley glacier that flows from the Andrei Icefield which dominates the mountains north of the Hoodoo River and from which numerous glaciers extend in all directions.

This large glacial field is named after the son of Olav Mokievsky-Zubok, a glaciologist who carried out significant glaciological work in the Coast Mountains from the 1960s to the 1970s.

About 3 km (1.9 mi) north of the Iskut River the Hoodoo River is joined by its main tributary, an unnamed stream flowing southeast from the glaciers of Surprise Mountain.