Tributaries
See also: List of tributaries of the Columbia RiverThe Salmon river is the second largest tributary. Although the Salmon has a larger drainage than the Clearwater, the Salmon drains much drier country and therefore has a smaller discharger than the Clearwater, about 8,000,000 acre feet (9.9 km3) annually compared to about 11,000,000 acre feet (14 km3) annually for the Clearwater river.
The Snake River has over twenty major tributaries, most of which are in the mountainous regions of the basin. The largest by far is the Clearwater River, which drains 9,000 square miles (23,000 km2) in north central Idaho. Many of the rivers that flow into the Snake River Plain from the north sink into the Snake River Aquifer, but still contribute their water to the river. Aside from rivers, the Snake is fed by many significant springs, many of which arise from the aquifer on the west side of the plain.
| Name | Length | Watershed size | Bank |
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| Heart River | 8.5 miles (13.7 km) | Right | |
| Lewis River | 12 miles (19 km) | Right | |
| Gros Ventre River | 642 square miles (1,660 km2) | Left | |
| Hoback River | 55 miles (89 km) | 600 square miles (1,600 km2) | Left |
| Greys River | 65 miles (105 km) | 800 square miles (2,100 km2) | Left |
| Salt River | 70 miles (110 km) | 890 square miles (2,300 km2) | Left |
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| Henrys Fork (Snake River) | 110 miles (180 km) | 3,212 square miles (8,320 km2) | Right |
| Portneuf River | 96 miles (154 km) | 1,329 square miles (3,440 km2) | Left |
| Raft River | 1,506 square miles (3,900 km2) | Left | |
| Malad River | 11.5 miles (18.5 km) | 3,000 square miles (7,800 km2) | Right |
| Salmon Falls Creek | 218 miles (351 km) | 2,082 square miles (5,390 km2) | Left |
| Bruneau River | 3,305 square miles (8,560 km2) | Left | |
| Boise River | 75 miles (121 km) | 4,100 square miles (11,000 km2) | Right |
| Owyhee River | 280 miles (450 km) | 11,049 square miles (28,620 km2) | Left |
| Malheur River | 165 miles (266 km) | 4,700 square miles (12,000 km2) | Right |
| Payette River | 62 miles (100 km) | 3,240 square miles (8,400 km2) | Right |
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| Weiser River | 90 miles (140 km) | 1,660 square miles (4,300 km2) | Right |
| Burnt River | 50 miles (80 km) | Left | |
| Salmon River | 425 miles (684 km) | 14,000 square miles (36,000 km2) | Right |
| Grande Ronde River | 212 miles (341 km) | 4,000 square miles (10,000 km2) | Left |
| Clearwater River | 80 miles (130 km) | 9,645 square miles (24,980 km2) | Right |
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| Tucannon River | 70 miles (110 km) | 503 square miles (1,300 km2) | Left |
| Palouse River | 140 miles (230 km) | 3,303 square miles (8,550 km2) | Right |
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