Although all of Idaho lies west of the continental divide, not all of its waters drain westward to the Pacific Ocean. A portion of southeast Idaho drains into Bear Lake, which is one of the largest interior drainage systems in the United States. In addition there are a number of isolated drainages in eastern Idaho that do not flow into the Snake or Bear Rivers that we term independent drainages. These include the Lost Rivers and Birch, Medicine Lodge, Beaver, and Camas Creeks.

The remainder of the state's surface drainage flows into the Columbia River. We have divided this system, from north to south, into the Kootenai, Pend Oreille, Spokane (Coeur d'Alene and St. Joe River systems), and the Palouse drainages. The Snake River and its tributaries drain areas upstream and downstream of Shoshone Falls. The major tributaries of the Snake River drainage below the falls include Salmon Falls Creek, and the Wood, Bruneau, Owyhee, Boise, Payette, Weiser, Salmon, and Clearwater Rivers. The Snake River above Shoshone Falls is comprised of the North Fork (Henry's Fork) and the South Fork. Major tributaries are the Teton, Blackfoot, and Portneuf Rivers.

The major natural lakes of Idaho include Priest and Pend Oreille (Pend Oreille drainage), Coeur d'Alene (Spokane drainage), Payette (Payette drainage, Snake River below Shoshone Falls), Gray's (Snake River above Shoshone Falls), Mud (independent drainage) and Bear (Bear River drainage). A large number of reservoirs have been formed on Idaho's rivers. The major ones include Dworshak (North Fork Clearwater River), Granite, Hells Canyon, Oxbow and Brownlee (Snake River, behind dams of the same name), Cascade (North Fork of the Payette River), Arrow Rock and Anderson Ranch, (Boise River), C. J. Strike (Snake River below Shoshone Falls), Blackfoot (Blackfoot River), Palisades (South Fork of the Snake River), and Island Park (Henry's Fork of the Snake River).

The Sawtooth Lakes include a number of high mountain lakes in the Sawtooth Mountains near the headwaters of the Salmon River. Numerous other smaller lakes and reservoirs dot Idaho's landscape.

The geological history of Idaho's drainages is not completely understood. Lava flows have changed the courses of many streams. Later the effects of glaciation formed both temporary and more permanent lakes. Glacial melting caused tremendous floods by breaching temporary dams and resulted in the alteration of river courses. Abandoned stream channels and dry waterfalls constitute evidence of these catastrophic events. These and other past geological phenomena have had a profound impact on the distribution of native Idaho fishes.

The Snake River at one time (probably prior to the Pleistocene) flowed down the middle of the Snake River Plain near the southern part of the U.S. Atomic Energy Commission Reservation (north of its present course). Subsequent downwarping and lava flows pushed the Snake River southeastward to its present course. Further uplifting and a rise of crustal divides along with deposition of large quantities of rock debris at the present southern reaches of the several drainage systems isolated the Lost Rivers and the other independent drainages of the area. These streams now flow generally in a southerly direction and sink into the permeable underground materials, including volcanic deposits, along the northern edge of the Snake River plain.

At a later time during the Pleistocene the immense inland Pluvial Lake Bonneville rose and overflowed into the upper Snake River through Red Rock Pass south of Pocatello, Bannock County. The first overflow occurred about 14,500 years ago. This great flood scoured out channels and water falls. After the flood the Bonneville Basin and the Snake River system were connected for a few thousand years until the lake fell below the Provo shoreline at 4800 feet.  A number of fishes from the Lake Bonneville fauna entered the upper Snake River in this manner. The present-day remnant of Pluvial Lake Bonneville is the Great Salt Lake.

In Northern Idaho during the Pleistocene, an ice lobe blocked the ancestral Clark Fork River and formed Glacial Lake Missoula, a huge lake that occupied much of the Clark Fork Valley all the way to Missoula, Montana.  Recent estimates are that forty separate times the ice dam formed by a valley glacier just east of Clark Fork, Idaho, broke, and huge floods occurred. The waters swept across eastern Washington toward the southwest and formed such features as Palouse Falls, the channeled scablands of eastern Washington, and Spokane Falls. These falls formed barriers to the post-glacial dispersal of fishes from the lower Columbia River, such as the Pacific salmon and steelhead trout. Falls on the Pend Oreille and Kootenai Rivers acted as similar barriers.