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Major river in the northwestern United States
the river in the northwestern United States

The Snake River is a major river in the interior Pacific Northwest region of the United States. About 1080 mile (1738 km) long, it is the largest tributary of the Columbia River, which is the largest North American river that empties into the Pacific Ocean. Beginning in Yellowstone National Park, western Wyoming, it flows across the arid Snake River Plain of southern Idaho, the rugged Hells Canyon on the borders of Idaho, Oregon and Washington, and finally the rolling Palouse Hills of southeast Washington. It joins the Columbia River just downstream from the Tri Cities, Washington, in the southern Columbia Basin. The river's watershed, which drains parts of six U. S. states, is situated between the Rocky Mountains to the north and east, the Great Basin to the south, and the Blue Mountains and Oregon high desert to the west. The region has a long history of volcanism; millions of years ago, Columbia River basalts covered vast areas of the western Snake River watershed, while the Snake River Plain was a product of the Yellowstone volcanic hotspot. The river was further altered by catastrophic flooding in the most recent Ice Age, which created such features as the Snake River Canyon and Shoshone Falls. The Snake River once hosted some of the largest North American runs of salmon and other anadromous fish. For thousands of years, salmon fishing has played a central role in the culture and diet of indigenous peoples. The Shoshone and Nez Perce were the largest of several tribes that lived along the river by the turn of the 19th century. The river's modern name comes from the Shoshone, who Plains Indians often called the "Snakes". In 1805, while searching for a route from the eastern US to the Pacific, Lewis and Clark became the first non natives to see the river. Fur trappers explored more of the watershed, and drove beaver to near extinction as the Americans and British vied for control of Oregon Territory. Although travelers on the Oregon Trail initially shunned the dry and rocky Snake River region, a flood of settlers followed gold discoveries in the 1860s, leading to decades of military conflict and the eventual expulsion of tribes to reservations. At the turn of the 20th century, some of the first large irrigation projects in the western US were developed along the Snake River. South central Idaho earned the nickname "Magic Valley" with the rapid transformation of desert into farmland. Numerous hydroelectric dams were also constructed, and four navigation dams on its lower section created a shipping channel to Lewiston, Idaho – the furthest inland seaport on the West Coast. While dam construction, commercial fishing and other human activities have greatly reduced anadromous fish populations since the late 19th century, the Snake River watershed is still considered important habitat for these fish. The Snake and its tributary, the Salmon River, host the longest sockeye salmon run in the world, stretching 900 mile (1448 km) from the Pacific to Redfish Lake, Idaho. Since the 1950s, public agencies, tribal governments and private utilities have invested heavily in fishery restoration and hatchery programs, with limited success. The proposed removal of the four lower Snake River dams for fish passage is a significant ongoing policy debate in the Pacific Northwest.

The Snake River begins on Two Oceans Plateau near the southern border of Yellowstone National Park, about 9200 feet (2804 m) above sea level in the Rocky Mountains of Wyoming. The Henrys Fork is sometimes called the "North Fork" of the Snake River,

Turning southwest, the river begins its long journey across the Snake River Plain, passing through Idaho Falls and receiving the Blackfoot River from the left before entering the 20 mile (32 km) long American Falls Reservoir, formed by American Falls Dam. Below Milner Dam it enters the Snake River Canyon of Idaho, where the river narrows, forming rapids and waterfalls. North of Twin Falls it plunges 212 feet (65 m) over Shoshone Falls, which in the spring flows with such force that 19th century writers called it the "Niagara of the West". In the 70 mile (113 km) stretch between Milner Dam and the confluence with the Malad River near Hagerman Fossil Beds National Monument, the Snake River descends a total of 1300 feet (396 m) over a series of cataracts, including Caldron Linn and Twin Falls above Shoshone Falls and Pillar, Auger, and Salmon Falls below it. Idaho Power operates several small hydroelectric plants along this stretch of the river. Uses of the name "Boise Valley" in this article, in a historical context, refer to the Treasure Valley.|group=n Passing 30 mile (48 km) west of Boise, it crosses briefly into Oregon before turning north to form the Oregon–Idaho border. Since its construction in 1967, Hells Canyon Dam has been the upriver limit for migrating salmon; in the past, salmon swam as far upriver as Shoshone Falls. Emerging from Hells Canyon Dam, the Snake surges northward through the Hells Canyon Wilderness, where the majority of the river corridor is accessible only by boat and numerous Class III IV rapids historically posed a major barrier to navigation. Today, the canyon and the surrounding Hells Canyon National Recreation Area are a popular location for whitewater boating, fishing, horseback riding and backpacking. Within the canyon it is joined from the left by the Imnaha River, then from the right by its longest tributary, the Salmon River. Further north, it begins to form the Idaho–Washington border, and receives the Grande Ronde River from the left. About 10 mile (16 km) downstream from Ice Harbor Dam, the Snake empties into the Columbia River at Burbank, Washington, southeast of the Tri Cities.

The U. S. Army Corps of Engineers has measured the discharge, or flow rate, of the Snake River at Ice Harbor Dam since 1962. The mean annual discharge for the 61 year period between 1962 and 2023 was , with a maximum recorded daily mean of on June 19, 1974 and a minimum daily mean of on November 29, 1961. In terms of discharge, the Snake River is the twelfth largest river in the United States, and it contributes about one fifth of the Columbia's total outflow into the Pacific. The volume of the Snake River peaks in late spring and early summer as snow melts in the Rocky Mountains, and reaches its lowest point in the fall. Despite the numerous dams regulating its flow, its discharge into the Columbia remains highly seasonal. Water from the lost streams of Idaho, several rivers that disappear underground in the eastern Plain, travels through the aquifer to reach the Snake River, as does excess irrigation water absorbed into the ground. At King Hill, about 50 mile (80 km) northwest of Twin Falls, water levels remain about for most of the year, increasing about 20 percent during snowmelt and decreasing about 20 percent with late summer irrigation diversions. Despite its great length, the Snake River accumulates most of its water in the lower one fourth of its course. By the time it reaches Hells Canyon Dam, 247 mile (398 km) from the mouth, the mean annual discharge is about – just over a third of the discharge at the mouth. Just two downstream tributaries, the Clearwater and Salmon Rivers, contribute about half of the total flow of the Snake. From the Lost Trail Pass north of Salmon, Idaho to Tri Basin Divide south of Afton, Wyoming, the eastern edge of the Snake River watershed follows the Continental Divide; as the Continental Divide also forms the Idaho–Montana border south of Lost Trail Pass, the Snake watershed touches Montana for a long distance, but does not extend into it. though the Columbia carries more than twice the volume of water. The Snake River watershed is very mountainous, with the northern two thirds of it occupied by vast mountain ranges of the Rockies, primarily the Salmon River Mountains of central Idaho and the Bitterroot Range along the Idaho–Montana border. The Blue Mountains form much of the western boundary of the Snake watershed from southeast Washington down into Oregon. To the south are numerous small isolated mountain ranges of the Basin and Range Province, such as the Independence and Albion Mountains. Surface volcanic features – such as lava fields, cones, and thermal springs – are replete in the southern part of the Snake watershed, from Craters of the Moon National Monument northeast of Twin Falls to the Yellowstone caldera, while ancient lava flows of the Columbia River basalts underlie the western part of the watershed. The Snake River Plain is the largest area without mountains, but it still features rugged terrain, being crisscrossed by canyons formed by the Snake River and its tributaries. Twin Falls experiences a semi arid climate, with about of rain and of snow. Monthly mean temperatures range from in January to in July. The Columbia Basin around the river's mouth also has a semi arid climate, with about of rain and of snow as measured at Ice Harbor Dam. January is the coldest month with a mean temperature of , and July is the hottest month at
Semi arid shrubland and rangeland covers about 50 percent of the Snake River watershed. Natural vegetation is primarily sagebrush, mixed with wheatgrasses and bunchgrasses. About 30 percent of the watershed is farmland; irrigated farming of potatoes, sugar beets, onions, cereal grains and alfalfa are dominant in the Snake River Plain, while the Palouse Hills of the northwest host mainly dryland wheat and legume production. Most of the Snake River watershed is public land, with the U. S. Forest Service managing the Nez Perce, Clearwater, Bitterroot, Umatilla, Wallowa Whitman, Payette, Boise, Salmon Challis, Sawtooth, Caribou Targhee and Bridger Teton National Forests that cover much of the northern and eastern parts of the watershed. The Snake River watershed borders several other major North American watersheds. To the south it borders the endorheic Great Basin, including the area draining to Utah's Great Salt Lake. To the east it borders the watersheds of the Green River, part of the Colorado River system which drains to the Sea of Cortez, and the Yellowstone and upper Missouri Rivers, part of the Mississippi River system which drains to the Gulf of Mexico. On the north it borders the watersheds of the Clark Fork and Spokane Rivers, both part of the Columbia River system. To the northwest it borders several other tributary watersheds of the Columbia River, including those of the John Day and Umatilla Rivers.

The present day course of the Snake River was pieced together over millions of years from several formerly disconnected drainage systems. Much of what would become the Pacific Northwest lay under shallow seas until it was uplifted starting about 60 million years ago (Ma). The outlet of the ancestral Columbia River to the Pacific was established about 40 Ma. By about 17 Ma, the "Salmon Clearwater River", or the modern day lower Snake River, flowed west into the Columbia and on to the Pacific. Another ancient river system drained what is now the western Snake River Plain. Some geologists propose that this flowed to the Columbia on a course south of the present day Blue Mountains, while others propose it drained towards Northern California. The Columbia River basalts, a series of massive flood basalt events that engulfed the Columbia Basin and surrounding lands, reshaped the landscape and erased most evidence of the pre volcanic river channels starting about 17 Ma. Erupting from fissures in the southern Columbia Basin, the first basalt flows pushed the ancient Salmon Clearwater much further north than its present course. About 12–10 Ma, the Blue Mountains region began to experience uplift, raising the basalt layers to form a plateau. From about 11–9 Ma, crustal deformation related to the Yellowstone hotspot caused the western half of the Snake River Plain to sink, creating a graben type valley between parallel fault zones to the northeast and southwest. The eastern half of the Snake River Plain formed as the North American Plate moved westward over the Yellowstone hotspot. Upwelling magma caused the continental crust to rise, forming highlands in a similar fashion to the modern Yellowstone plateau and leaving behind enormous basalt flows in its wake. As the hotspot migrated east relative to the North American Plate, the land behind it collapsed and sank, creating the geographic depression of the eastern Snake River Plain. The gradual eastward migration of this topographic high had the effect of pushing the Continental Divide to the east. Prior to the formation of the eastern Snake River Plain, the drainage area east of about Arco, Idaho – the modern headwaters and upper course of the Snake River – flowed towards the Atlantic Ocean via the Mississippi River system. In the Columbia Basin about 10.5 Ma, the Elephant Mountain basalt eruption forced the Salmon Clearwater River into roughly its present course through southeast Washington. By 8.5 Ma the Salmon Clearwater was established in the Columbia River's modern path through Wallula Gap, although the Columbia itself still flowed somewhere to the west. The last of the Columbia basalt flows occurred around 6 Ma; by then, the present day confluence of the Columbia River and Salmon Clearwater had been established, with the combined flow draining through Wallula Gap. The Teton Range, a defining topographic feature of the modern Snake River headwaters, first began to rise about 10 Ma as the Teton Fault began to move, displacing the mountain block upward as the surrounding land dropped. About 2 Ma, the Hoback Fault formed east of the Tetons, and a graben valley developed between the Hoback and Teton fault zones, creating Jackson Hole. As the valley dropped, water filled it to create Lake Teewinot, which drained east into the Green River–Colorado River system. About 1 Ma, the Snake River captured the Jackson Hole watershed, draining Lake Teewinot and finally connecting the modern day Snake headwaters to the rest of the river. This landscape around the Snake headwaters was sculpted by multiple Ice Age glaciations. Starting about 200,000 years ago, the Buffalo glaciation filled Jackson Hole to a depth of 2000 feet (610 m). Ice flowed down the Snake River Canyon all the way to Idaho. The flood completely altered the landscape of the Snake River Plain, creating the Snake River Canyon and its waterfalls, vast boulder fields, cliffs and coulees. The floodwaters then emptied through Hells Canyon; however, most evidence of their effects on the lower Snake River was erased by the much larger Missoula Floods that engulfed the Columbia Basin during the same period.

Starting around the end of the last glacial period, the Snake River Plain was inhabited by hunter gatherers of the ancient Clovis (10000–9000 BCE), Folsom (9000–8000 BCE) and Plano (8600–5800 BCE) cultures. Along the lower Snake River in Washington, the Marmes Rockshelter – flooded in 1968 after the construction of Lower Monumental Dam – has yielded archeological evidence of continuous human occupation from about 9000 BCE until about 1300 CE. Starting about 2200 BCE, people in the western Snake River basin began to adopt a semi sedentary lifestyle, with an increased reliance on fish (primarily salmon) and food preservation and storage. Shoshoni speaking peoples arrived in the Snake River Plain between 600 and 1500 CE. The Northern Shoshone and the Bannock, a Northern Paiute group that became culturally associated with the Shoshone, occupied an area stretching from the Snake River Plain east to the Rocky Mountains and south towards the Great Basin, as well as valleys of the upper Salmon River. Another Nez Perce name for the Snake River was Pikúunen, specifically referring to the stretch upstream of the Clearwater confluence. The Wanapum and Walla Walla people called the lower Snake River below the Clearwater Naxíyam Wána. The Shoshone called the river Yampapah, after the yampah plant that grew profusely along its banks. Downriver of Shoshone Falls, salmon and their cousins such as steelhead trout – anadromous fish which spend their adult lives in the ocean, returning to fresh water to spawn – were a key food source for indigenous peoples, and were of great cultural importance. Rituals such as the first salmon ceremony were widely observed along the Columbia, Snake and other Northwest rivers, and so were strict catch limits, such that a healthy number of salmon would survive to reach their natal streams. The Nez Perce had more than seventy permanent villages among their fishing grounds on the Snake, Clearwater and Salmon Rivers. Clans gathered at communal fishing sites starting about May or June. Fishing moved from the lower rivers to higher elevation streams throughout the summer, while fall run fish were preserved for winter use. Shoshones in the western part of the Snake River Plain also depended heavily on the salmon run. At Shoshone Falls and the smaller cataracts downstream, fishing platforms, temporary brush weirs, spears, baskets and fish traps were employed at large scale. Captain Benjamin Bonneville in 1832 observed that "Indians at Salmon Falls on the Snake River took several thousand salmon in one afternoon by means of spears." To the east and upriver of the falls, many Shoshone and Bannock lived in more nomadic groups, traveling to the falls during the spring salmon run then gathering camas bulbs and hunting bison through the summer and autumn months. The Snake River at Hells Canyon formed a natural dividing line between the Nez Perce and Shoshone, who considered each other enemies. The Nez Perce allied with the Cayuse against the Shoshone, Bannock and Northern Paiute, and stopped the latter from expanding their territory towards the Columbia Plateau. Both the Nez Perce and Shoshone acquired horses in the late 1600s or early 1700s, enabling far reaching trade and hunting expeditions. With horses, the Nez Perce were able to travel east of the Bitterroot Mountains to hunt bison, via the trail over Lolo Pass, which the Lewis and Clark expedition would later follow in order to reach the Snake and Columbia Rivers. The Shoshone, Bannock and Northern Paiute were referred to by Great Plains tribes as the "Snakes", possibly in reference to the use of snake heads in war or because the Plains tribes referred to these groups with a snake like hand gesture, possibly originally intended to indicate a salmon. The English name for the river was likely derived from an interpretation of this hand gesture, although it is uncertain when the name was first used.

The first Euro Americans to reach the Snake River watershed were the Lewis and Clark Expedition, who in August 1805 crossed the Continental Divide at Lemhi Pass and descended to the Salmon River at what is now Salmon, Idaho, naming the stream "Lewis's River". Thwarted by the river's rapids, they were forced to cross the Bitterroot Mountains via the Nez Perce trail at Lolo Pass. After paddling down the Kooskooskee (Clearwater River), they reached the junction with the Snake and camped there with the Nez Perces on October 10, 1805. They correctly surmised that the river coming from the south was a continuation of "Lewis's" or Salmon River. The expedition journals note the Nez Perce called it Kimooenim, although William Clark later erased mentions of the name to replace with "Lewis's". Other explorers quickly followed, many of them fur trappers who began scouting the upper Snake River watershed for beaver. John Colter, a former member of the Lewis and Clark expedition, explored the Jackson Hole area in 1808. In 1810, Andrew Henry explored and named the Henrys Fork of the Snake River. He established Fort Henry, the first American fur trading post west of the Rocky Mountains, but abandoned it after that year's harsh winter. A group led by Robert Stuart, a member of the Hunt expedition, returned eastward across the plain the following year. The route they mapped would eventually become that section of the Oregon Trail. In 1818 Donald Mackenzie and Alexander Ross established Fort Nez Percés for the North West Company near the confluence of the Snake and Columbia Rivers. The following year, Mackenzie traveled up the Snake River and reached Boise Valley by making the first recorded river ascent of Hells Canyon. As American fur trappers kept coming to the region, the HBC ordered the Canadians to kill as many beavers as they could, under the rationale that "if there are no beavers, there will be no reason for the Yanks to come," and even if the Americans did ultimately gain control, the HBC would already have taken all the profit. Starting in the 1840s, the Oregon Trail became well established, and thousands of settlers passed through the Snake River Plain on their way to the Willamette Valley. Coming from Wyoming, the Oregon Trail reached the Snake River at Fort Hall, Idaho, and stayed south of the river until Three Island Crossing near modern day Glenns Ferry. Here the trail diverged, with the northern route fording the river to reach the HBC trading post at Fort Boise while the southern route continued into what is now the eastern Oregon desert. While the northern route passed through more favorable country, the Snake River posed a formidable barrier; during high water, many travelers were forced to take the hot, dry southern route, or risk drowning. Travelers going via Fort Boise had to cross the river one more time to rejoin the trail heading west. A ferry existed at Fort Boise since at least 1843; the Three Island crossing was also replaced by a ferry in 1869.

As the flow of settlers increased, the Nez Perce and their neighbors the Cayuse and Walla Walla came under pressure to cede portions of their territory. Tensions flared in 1855 after tribes relinquished huge amounts of territory in the Treaty of Walla Walla. The sternwheeler Colonel Wright was commissioned to haul supplies up the Snake River to Fort Taylor. Captained by veteran Oregon river pilot Len White, the Wright was the first steamboat to run on the Snake River and the Columbia above The Dalles. While early settlers had simply passed through this area on their way to Oregon, gold strikes brought renewed interest in the 1860s. The Army rebuilt Fort Boise further east of the original site in 1863. A military detachment was stationed there to quell any further violence; however, tensions continued to increase, and more wagon trains and mining parties were attacked. Starting in 1864, the Snake War was fought across much of southern Idaho, with numerous battles between the U. S. Army and the Shoshone, Bannock and Paiute. By 1868, exhausted after years of fighting, Chief Pocatello and many others surrendered and relocated to the Fort Hall Indian Reservation on the Snake River in southeast Idaho. Tribal resistance would continue for years to come. In 1877 the US government attempted to force the remaining Nez Perce onto their reservation, at which point Chief Joseph's band and several others opted to seek refuge elsewhere. After a treacherous crossing of the Snake at Dug Bar, Hells Canyon on May 31, the Nez Perce were pursued by the Army for over 1000 mile (1609 km) east, through Yellowstone before turning north through Montana, fighting several battles along the way. On October 5, 1877, Chief Joseph surrendered to US forces. thus ending the Nez Perce War. The survivors were distributed to various reservations across the western US. In 1878, an uprising occurred in response to overcrowding and food shortages at the Fort Hall Reservation, leading to the Bannock War. The US army defeated the Bannock and their Paiute allies and proceeded to restrict travel in and out of the reservation. While Lewiston was now well connected by river, travel to Boise and other points upstream on the Snake River remained difficult due to the formidable obstacle of Hells Canyon. In 1865, Thomas Stump attempted to pilot the Colonel Wright up Hells Canyon, making it 80 mile (129 km) upriver before hitting rocks in a rapid, forcing their retreat. In addition to commerce, the railroad also opened the Snake River region – which just a few years ago had been seen as a remote, rough frontier – to recreation. The Union Pacific heavily promoted tourism in places like Shoshone Falls, Payette Lake and Soda Springs, Idaho. Countering the reputation of southern Idaho as a wasteland, a brochure described Shoshone Falls, "Shoshone differs from every other waterfall in this or the old country. It is its lonely grandeur that impresses one so deeply; all of the other historic places have the adjuncts of civilization, and one is almost overshadowed by a city while in their presence."

Most travelers on the Oregon Trail regarded the arid Snake River Plain as an obstacle to be crossed, not a land to be settled. This began to change with the Boise gold strikes, where the demands of the mining industry and the difficulty of importing goods set off an agricultural boom in the Boise Valley. The dry climate made irrigation necessary, and numerous private irrigation companies were formed. Private canal systems around Boise and Idaho Falls saw some success, but all the easily farmable land was soon developed, and they could not raise the capital for further expansion. In addition, low water by late summer posed a challenge to farmers, and the irrigation companies could not afford to build dams to provide water storage. With many private irrigation companies verging on insolvency, the federal government began to explore programs assisting agricultural development. The 1894 Carey Act granted large tracts of dry federal land to western states, which then sold the land to farmers and solicited private investors to organize irrigation districts. Investors would then recoup their capital by selling water rights to farmers. I. B. Perrine, who homesteaded near Shoshone Falls in the 1880s, went on to develop one of the most successful Carey Act projects. In 1900 Perrine filed a claim for water from the Snake River, and backed by significant private capital, oversaw the construction of Milner Dam and a canal system to irrigate some of the Snake River Plain. During certain times of the year, almost all the Snake River's flow was diverted at Milner Dam, and since then, Shoshone Falls has regularly run dry in the summer. The Idaho State Historical Society writes that "Perrine’s venture contrasted remarkably with private canal company failures that led to congressional provision for federal reclamation projects after 1902. As a rare successful example of state supervised private irrigation development provided for in [the Carey Act] of 1894, Milner Dam and its canal system have national significance in agricultural history." With the creation of the Reclamation Service (now the Bureau of Reclamation) in 1902, the federal government began to play a more direct role in water resources development. The expansive Minidoka Project was the first federal reclamation project in Idaho. Starting with Minidoka Dam in 1906, the project would grow over the next few decades to include major reservoirs at Jackson Lake, American Falls and Island Park, and a large network of canals and pump stations. The Minidoka Project would eventually bring water to a million acres (2,500 km2) of the Magic Valley. Starting around the 1950s, farmers made heavy use of the Snake River aquifer, bringing large new areas into production. Near Rexburg, the Teton Dam was also built to provide water for this area. In 1976, the Teton Dam failed catastrophically, killing eleven people and causing at least $400 million in damage along the Henrys Fork and Snake Rivers. The political fallout from this disaster marked the end of large new irrigation developments not only for the Snake River system, but for the Bureau of Reclamation as a whole. Agriculture has significantly impacted water quality in the Snake River upstream of Hells Canyon. Water removed from the river for irrigation becomes contaminated with chemical fertilizers and manure, and percolates into the Snake River Aquifer. Pollutants collect in the groundwater and eventually enter the river via spring flows. Excess nitrogen, phosphorus and bacterial loads occur in many locations across southern Idaho. Large algae blooms are a recurring issue in summer. The U. S. Environmental Protection Agency has established water quality guidelines for Snake River flows entering Hells Canyon, which cover bacteria, mercury, excess nutrients, pesticides, sediments and water temperature. Implementation of the guidelines include best management practices for agriculture and forestry, and regular water quality monitoring.

Power development of the Snake River began in the early 20th century as cities, farms, mines and industry grew around the river. The first small hydroelectric plant on the Snake River, Swan Falls Dam, was built in 1901, followed by one at American Falls in 1902. Small private utilities built power plants at Salmon Falls (1910) and Thousand Springs (1912). Idaho Power was incorporated in 1915, and acquired all the aforementioned plants the following year. It proceeded to build a second, larger plant at Shoshone Falls in 1921, and another plant at Twin Falls in 1935. The advent of electric pumps opened up large new areas to agriculture, which had previously been limited to land where water could flow by gravity. The Minidoka Project, which included the Bureau of Reclamation's first hydroelectric plant in Idaho, was an early adopter of this system. The project generated more power than it needed, and surplus was sold to nearby towns such as Burley and Rupert, which created their own municipal electric systems. By the 1940s, following the construction of massive hydropower dams on the Columbia River such as Grand Coulee, interest turned to the considerable untapped power potential of the Snake River in Hells Canyon. In 1947, Idaho Power set its sights on the upper section of the canyon, where it proposed a series of three medium sized dams. Two years later, the U. S. Army Corps of Engineers (Army Corps) proposed a single massive dam, over 700 feet (213 m) high, to be built in lower Hells Canyon. In 1955 the Federal Power Commission authorized the Idaho Power project, but initially only one of the three dams, Brownlee (completed 1958), was built. The other dams, located downstream, would have been in the flood zone of not only the Army Corps' high dam, but two other competing proposals. By then, significant public opposition had formed against the high dam, as it would still block salmon migration to the upper Snake, and adversely affect wildlife and recreational values in Hells Canyon. It was also challenged by Washington Public Power, which argued that the Commission should give priority to public utilities over private ones. This was the first time the court cited environmental protection as a consideration for whether to approve a dam project. and produce about 6,053 gigawatt hours per year. Idaho Power's hatcheries produce almost seven million salmon and steelhead smolt to release in the Snake River system each year. Since the completion of the Hells Canyon complex, with the exception of the lower Snake River dams, only one major hydroelectric dam has been built in the Snake River system – the Army Corps' Dworshak Dam (1973), in the Clearwater River basin. Like the Hells Canyon dams, Dworshak also generated controversy over its impact on fisheries, and also made no provision for fish passage; rather, a hatchery was built at the base of the dam.

As gold mining declined in the late 19th century, the wheat industry boomed in the Palouse of southeast Washington. By the 1870s, the Oregon Steam Navigation Company was operating seven steamboats transporting grain from the Snake River to lower Columbia River ports. These were the Harvest Queen, John Gates, Spokane, Annie Faxon, Mountain Queen, R. R. Thompson, and Wide West. In the 1890s, a huge copper deposit was discovered at Eureka Bar in Hells Canyon. Several ships transported ore from there to Lewiston, including Imnaha, Mountain Gem, and Norma. The IEWA initially pushed for improvements such as bigger locks at Bonneville Dam in 1938 and the construction of McNary Dam on the Columbia, which would improve navigation to the mouth of the Snake. The Lower Monumental project generated controversy as it threatened to flood the Marmes Rockshelter archeological site. Although the Army Corps agreed to build a dike around the site, it began to leak as the reservoir filled and the site was inundated. By the 1970s, the environmental movement in the US had become significantly larger, and groups such as the Association of Northwest Steelheaders lobbied to stop the construction of the fourth dam, Lower Granite. These efforts were unsuccessful, and the dam was completed in 1975. The first upriver barge reached Lewiston on April 10 of that year. Once the dams were completed, barges up to 12,000 tonnes and drawing 14 feet (4 m) of water were able to reach Lewiston. Today, multiple barge terminals operate along the lower Snake, including Lewiston, Clarkston, Wilma, Central Ferry and Almota. Since 2000, the tonnage of commercial shipping on the Snake River has declined, due mostly to the loss of petroleum products after a pipeline was constructed. After the general decline of the Great Recession, other sectors have been slow to recover. As of 2015, grain tonnage had fallen about a third from 2000 levels, while forestry products had fallen by nearly three quarters, with many shipments switching back to rail. Container shipping at the Port of Lewiston ceased in 2015, due to its primary source, the Port of Portland, no longer receiving containers. From 2015 to 2023, grain exports from the Port of Lewiston have remained relatively steady while breakbulk cargo has increased. As dam opponents had feared, Snake River salmon returns declined greatly after the dams were built. Since 2000, there have been renewed calls for removing the lower Snake River dams, which have become a significant political issue for the Pacific Northwest.

The World Wide Fund for Nature (WWF) divides the Snake River into two freshwater ecoregions – the Upper Snake and Columbia Unglaciated – with Shoshone Falls marking the boundary between the two. Shoshone Falls has presented a total barrier to the upstream movement of fish at least since the Bonneville flood 15,000 years ago. The Big Wood River (the main tributary of the Malad River) is also included in the Upper Snake ecoregion, due to the presence of a separate natural waterfall barrier. As a result, only 35 percent of the fish fauna above Shoshone falls, and 40 percent of the Big Wood River's fish fauna, are shared with the lower Snake River. Compared to the lower Snake River and the rest of the Columbia River system, the Upper Snake ecoregion has a high level of endemism, especially among freshwater molluscs such as snails and clams. At least 21 snail and clam species are of special concern, including 15 that appear to exist only in single clusters. The Snake River below Shoshone Falls is home to about 35 native fish species, of which 12 are also found in the Columbia River and four of which are endemic to the Snake or nearby watersheds: the sand roller, shorthead sculpin, margined sculpin and the Oregon chub, which also occurs in a few other Oregon streams. Large white sturgeon, introduced to the Snake River in the 19th century, were once widespread in the Snake River below Shoshone Falls; due to dam construction, only a few fragmented populations remain. Other common introduced species include whitefish, pikeminnow, smallmouth bass, and rainbow, brown, brook and lake trout. Salmon die after spawning, and their carcasses represent a crucial influx of organic matter to mountain rivers that have few natural nutrient sources. The Snake River produced about 40 percent of all chinook salmon and 50 percent of all steelhead in the Columbia River watershed. Populations further collapsed once dams were built on the lower Snake and Columbia Rivers, and Hells Canyon Dam blocked access to the upper Snake. Wild Snake River spring and summer chinook returns declined from 130,000 in the 1950s to less than 5,000 in the 1990s. Wild steelhead returns followed a similar pattern, falling from 110,000 in the 1960s to less than 10,000 in the 1990s. Spring, summer and fall run chinook were all listed as threatened in 1992. Snake River steelhead were also listed as threatened in 1997. While coho had disappeared from the Snake River by the 1980s, reintroduction efforts since 1995 have seen success. Snake River sockeye once numbered to up 150,000 adults. Between 24,000–30,000 sockeye returned to Wallowa Lake in the Grande Ronde River watershed, but the run was eliminated by 1905 due to overharvest and unscreened irrigation diversions. The Payette Lake population once numbering up to 100,000 was blocked by the Black Canyon Dam in 1924. Snake River sockeye were listed as endangered in 1991. Wild chinook salmon and steelhead continued to decline into the 1990s, but have begun an unsteady recovery since 2000, with both chinook and steelhead returns up to 20,000–30,000 in some years. Hatcheries release about 33 million salmon and steelhead smolt into the Snake River watershed each year. Upstream of the four lower dams, the Snake River watershed contains some of the best remaining spawning habitat in the Columbia River system, particularly along the Clearwater and Salmon Rivers; the latter is one of the longest undammed rivers in the continental US.

The Snake River provides important wildlife habitat along much of its course, particularly in the arid Snake River Plain where it is the only source of water for many miles. The upper reaches of the Snake River, including in Jackson Hole and the floodplain north of Idaho Falls where it joins the Henrys Fork, have significant riparian gallery forests dominated by black cottonwood and narrowleaf cottonwood. Part of these wetlands were flooded with the construction of American Falls Dam, and large portions of the remainder have been degraded by cattle grazing. On the Snake River south of Boise is the nearly Morley Nelson Snake River Birds of Prey National Conservation Area, which hosts the densest concentration of nesting raptors in the US. The Snake River headwaters are part of the Greater Yellowstone Ecosystem, which the National Park Service describes as "one of the largest nearly intact temperate zone ecosystems on Earth." The region is home to some of the largest wild elk and bison populations in the US, and provides habitat for grizzly bear, wolverine and lynx. The other major wild area in the Snake River watershed centers on Idaho's extremely rugged Frank Church–River of No Return Wilderness, the largest federally designated wilderness in the contiguous US. and on the Clearwater River, which hosted the last whitewater log drive in the US in 1971. Logging is still a major industry in the region, though since the 1990s, logging south of the Clearwater has decreased. Large areas of native sagebrush steppe ecosystems, mostly in the Snake River Plain and Palouse, have been developed for agriculture. About two thirds of the Snake River Plain remains grassland or shrubland; however, much of this acreage is impacted by livestock grazing, and fire regimes have become more severe with the proliferation of invasive species like cheatgrass.

The lower Snake River dams have remained controversial since their construction, and in the 21st century there has been increased debate over potentially removing the dams. Although the dams were built with fish ladders, the warm, slow moving water in reservoirs disoriented migrating fish, and juvenile fish experienced significant mortality passing through the dams. efforts to capture fish and transport them around the dams have seen little success. There are other economic arguments for dam removal, particularly that the annual cost of maintaining the barge channel exceeds the economic benefits provided by shipping, and the freight can be moved by rail instead. Furthermore, the dams only account for a small percentage of the total hydropower in the Northwest. though Simpson's plan has come under scrutiny as among other actions, it would also impose "a 35 year moratorium on litigation related to anadromous fish" at federal Columbia River Basin dams. Opponents of dam removal include farmers, local governments such as the city of Lewiston, congressional representatives in eastern Washington and the Bonneville Power Administration, which manages federal hydroelectric dams in the Northwest. While the dams do not generate much baseload power, they are crucial to managing peak demand on a daily basis, as hydropower can be ramped up and down quickly. As more wind and solar energy is added to the Northwest grid, more load balancing will be needed to compensate for the intermittent nature of those sources. Although Washington governor Jay Inslee and Washington Senator Patty Murray have tentatively endorsed dam removal, they stressed that hydropower must be replaced by other renewable sources, and economic impacts such as the loss of the ship channel should be "mitigated or replaced." In December 2023, the Biden administration expressed its support for the Columbia Basin Restoration Initiative, which would develop a strategy to replace the power and navigation benefits provided by the Snake River dams, and explore options for post dam river restoration. The initiative is an agreement between the federal government, four tribal nations, the states of Washington and Oregon, and several conservation groups. It would not authorize the removal of the dams, which would require a separate act of Congress.