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Dam-building era

In the late 19th and early 20th centuries, a great number of dams were built along the course of the Missouri, transforming 35 percent of the river into a chain of reservoirs. River development was stimulated by a variety of factors, first by growing demand for electricity in the rural northwestern parts of the basin, and by floods and droughts that plagued rapidly growing agricultural and urban areas along the lower Missouri River. Small, privately owned hydroelectric projects have existed since the 1890s, but the large flood-control and storage dams that characterize the middle reaches of the river today were not constructed until the 1950s.

Between 1890 and 1940, five dams were built in the vicinity of Great Falls to generate power from the Great Falls of the Missouri, a chain of giant waterfalls formed by the river in its path through western Montana. Black Eagle Dam, built in 1891 on Black Eagle Falls, was the first dam of the Missouri. Replaced in 1926 with a more modern structure, the dam was little more than a small weir atop Black Eagle Falls, diverting part of the Missouri's flow into the Black Eagle power plant. The largest of the five dams, Ryan Dam, was built in 1913. The dam lies directly above the 87-foot (27 m) Big Falls, the largest waterfall of the Missouri.

In the same period, several private establishments – most notably the Montana Power Company – began to develop the Missouri River above Great Falls and below Helena for power generation. A small run-of-the river structure completed in 1898 near the present site of Canyon Ferry Dam became the second dam built on the Missouri. This rock-filled timber crib dam generated seven and a half megawatts of electricity for Helena and the surrounding countryside. The nearby steel Hauser Dam was finished in 1907, but failed in 1908 because of structural deficiencies, causing catastrophic flooding all the way downstream past Craig. At Great Falls, a section of the Black Eagle Dam was dynamited to save nearby factories from inundation. Hauser was rebuilt in 1910 as a concrete gravity structure, and stands to this day.

Holter Dam, about 45 miles (72 km) downstream of Helena, was the third hydroelectric dam built on this stretch of the Missouri River. When completed in 1918 by the Montana Power Company and the United Missouri River Power Company, its reservoir flooded the Gates of the Mountains, a limestone canyon which Meriwether Lewis described as "the most remarkable clifts that we have yet seen... the towing and projecting rocks in many places seem ready to tumble on us." In 1949, the U.S. Bureau of Reclamation (USBR) began construction on the modern Canyon Ferry Dam to provide flood control to the Great Falls area. By 1954, the rising waters of Canyon Ferry Lake submerged the old 1898 dam, whose powerhouse still stands underwater about 1 + 1 ⁄ 2 miles (2.4 km) upstream of the present-day dam.

"uncertain as the actions of a jury or the state of a woman's mind".

The Missouri basin suffered a series of catastrophic floods around the turn of the 20th century, most notably in 1844, 1881, and 1926–1927. In 1940, as part of the Great Depression -era New Deal, the U.S. Army Corps of Engineers (USACE) completed Fort Peck Dam in Montana. Construction of this massive public works project provided jobs for more than 50,000 laborers during the Depression and was a major step in providing flood control to the lower half of the Missouri River. However, Fort Peck only controls runoff from 11 percent of the Missouri River watershed, and had little effect on a severe snowmelt flood that struck the lower basin three years later. This event was particularly destructive as it submerged manufacturing plants in Omaha and Kansas City, greatly delaying shipments of military supplies in World War II.

Flooding damages on the Mississippi – Missouri river system were one of the primary reasons for which Congress passed the Flood Control Act of 1944, opening the way for the USACE to develop the Missouri on a massive scale. The 1944 act authorized the Pick–Sloan Missouri Basin Program (Pick–Sloan Plan), which was a composite of two widely varying proposals. The Pick plan, with an emphasis on flood control and hydroelectric power, called for the construction of large storage dams along the main stem of the Missouri. The Sloan plan, which stressed the development of local irrigation, included provisions for roughly 85 smaller dams on tributaries.

In the early stages of Pick–Sloan development, tentative plans were made to build a low dam on the Missouri at Riverdale, North Dakota, and 27 smaller dams on the Yellowstone River and its tributaries. This was met with controversy from inhabitants of the Yellowstone basin, and eventually the USBR proposed a solution: to greatly increase the size of the proposed dam at Riverdale – today's Garrison Dam, thus replacing the storage that would have been provided by the Yellowstone dams. Because of this decision, the Yellowstone is now the longest free-flowing river in the contiguous United States. In the 1950s, construction commenced on the five mainstem dams – Garrison, Oahe, Big Bend, Fort Randall, and Gavins Point – proposed under the Pick-Sloan Plan. Along with Fort Peck, which was integrated as a unit of the Pick-Sloan Plan in the 1940s, these dams now form the Missouri River Mainstem System.

The flooding of lands along the Missouri River heavily impacted Native American groups whose reservations included fertile bottomlands and floodplains, especially in the arid Dakotas where it was some of the only good farmland they had. These consequences were pronounced in North Dakota's Fort Berthold Indian Reservation, where 150,000 acres (61,000 ha) of land was taken by the construction of Garrison Dam. The Mandan, Hidatsa and Arikara / Sanish tribes sued the federal government on the basis of the 1851 Treaty of Fort Laramie which provided that reservation land could not be taken without the consent of both the tribes and Congress. After a lengthy legal battle the tribes were coerced in 1947 to accept a $5.1 million ($55 million today) settlement for the land, just $33 per acre. In 1949 this was increased to $12.6 million. The tribes were even denied the right to use the reservoir shore "for grazing, hunting, fishing, and other purposes".

The six dams of the Mainstem System, chiefly Fort Peck, Garrison, and Oahe, are among the largest dams in the world by volume; their sprawling reservoirs also rank among the biggest of the nation. Holding up to 74.1 million acre-feet (91.4 km) in total, the six reservoirs can store more than three years' worth of the river's flow as measured below Gavins Point, the lowermost dam. This capacity makes it the largest reservoir system in the United States and one of the largest in North America. In addition to storing irrigation water, the system also includes an annual flood-control reservation of 16.3 million acre-feet (20.1 km). Mainstem power plants generate about 9.3 billion KWh annually – equal to a constant output of almost 1,100 megawatts. Along with nearly 100 smaller dams on tributaries, namely the Bighorn, Platte, Kansas, and Osage Rivers, the system provides irrigation water to nearly 7,500 sq mi (19,000 km) of land.

The table at left lists statistics of all fifteen dams on the Missouri River, ordered downstream. Many of the run-of-the-river power generation dams on the Missouri (marked in yellow) form very small impoundments which may or may not have been given names; those unnamed are left blank. All dams are on the upper half of the river above Sioux City; the lower river is uninterrupted due to its longstanding use as a shipping channel.