New Life for the Mighty Mo

In the name of progress, man spent much of the past century taming the Missouri River. Now, we're having second thoughts.

With six dams, we flooded a third of the Missouri's historical bottomland, and straightened and deepened the lower third of the river into a channel for commercial navigation. Only a third of Mighty Mo's 2,341 miles now remains in a natural or semi-natural state. In some ways the work has paid huge dividends, including billions of dollars in flood control. But, there were losses, too.

When the dams and channel were built, some people knew fish and wildlife habitat would be lost. Such costs were considered the price of progress. But most did not appreciate the real value of a healthy and incredibly diverse river ecosystem until recently. The nation's values have changed, and today many want to see some of man's work and its damage to the river undone. They want a more natural flow to breathe life back into what is now a very sick river.

During the past 14 years, competing visions for the Missouri have fueled a debate about the U.S. Army Corps of Engineers work to revise the Missouri River Master Water Control Manual, the

A meandering side-channel chute, restored at Hamburg Bend Wildlife Management Area near Nebraska City in 1996 as part of the Missouri River Fish and Wildlife Mitigation Project, provides valuable fish and wildlife habitat in the channelized reach of the river.

blueprint the Corps follows in managing the river. The U.S. Fish and Wildlife Service (USFWS) has said the Corps' current management practices jeopardize three federally threatened or endangered species - the interior least tern, piping plover and pallid sturgeon - as well as other native species. It recommended that a semblance of the river's natural flows be restored, including a spring rise and a low summer flow.

Environmental interests, including the Nebraska Game and Parks Commission, which manages the state's fish and wildlife resources, support proposed flow changes. Agricultural, navigation and other interests want things to stay as they are. To say the debate pits the environment against agriculture and industry is true, but it oversimplifies the issue. Many have stakes in the issue, including those who live along the river in Nebraska and elsewhere, and those who have gained or lost because of changes to the river.

The Missouri River forms at Three Forks, Montana, where the Jefferson, Madison and Gallatin rivers flow from the Bitterroot Mountains. The nation's longest river, the Missouri drains 530,000 square miles in 10 states and part of Canada.

Not long ago, many described the Missouri River as a sleeping giant. Each spring, when the snow melted on the plains and the spring rains came, the river raged. A boiling mass of mud and sand, it chewed its way through the soft alluvial bottomland soils, and wreaked havoc with anything in its path through Montana, North and South Dakota, Nebraska, Iowa, Kansas and Missouri to the Mississippi River at St. Louis. Soon the early spring flows would subside, but when the snow in the Rocky Mountains melted, another surge of water would come. By today's standards, a 100-year flood occurred every three years on the Missouri before the dams were built.

George Fitch wrote about the river in American Magazine in 1907: "It makes farming as fascinating as gambling too. You never know whether you are going to harvest corn or catfish. The farmer may go blithely forth in the morning with a twine binder to cut his wheat only to come back at noon for a trotline - his wheat having gone down the river the night before.

"These facts lead us naturally to the subject of the Missouri's appetite. It is the hungriest river ever created. It is eating all the time - eating yellow clay banks and cornfields, eighty acres at a mouthful; winding up its banquet with a truck garden and picking its teeth with the timbers of a big red barn. It's yearly menu is ten thousand acres of good, rich farming land, several miles of railroad and a few houses, a forest or two and uncounted miles of sandbars."

After the spring rises, the river would become a lazy meander, except during occasional downpours, for the rest of the year. It still chewed its banks, but took smaller bites. The river's appetite for soil gave it one of its many nicknames, the Big Muddy. Often said to be too thick to drink and too thin to plow, the river was "the muddiest stream in the world," according to Fitch, who said it was, "so thick that it cracks, sometimes, in working its way around the bends."

In winter, ice halted the river's flow on the surface. In spring, when the ice broke up, the huge shards would form ice dams. Where the river couldn't break through, it went around, spilling water over the floodplain.

Erosion and flooding are natural processes of all rivers. The Missouri was better at it than most. The river's rages created some of the most diverse habitat for fish and wildlife found anywhere. It made wide, sweeping bends through its valley, which ranges from two to 20 miles wide in Nebraska. As the river cut away outer banks, it deposited soil on inner banks, causing bends to grow wider. Meriwether Lewis and William Clark, on their journey upriver in 1804, calculated that around one bend now near Decatur, Nebraska, the river flowed 18¾ miles to cover 974 yards. These loops were often breached, creating oxbow lakes no longer connected to the river.

Flood pulses would reshape sandbars and islands and scour them clean of vegetation. When the flows receded, a braided, sinuous river remained - a swift and deep main channel, shallow side channels and chutes, and slowly moving or still water in backwaters and sloughs. Countless sandbars, which

A river tow pushes two barges down the channelized Missouri River below Indian Cave State Park. River barge traffic has not met original projections, causing many to question the value of continued support for the industry.

became habitat to the least tern, piping plover and other shorebirds, dotted the river. Where the river found a new channel, its old one became a trail of wetlands, lakes and marshes that were filled by flooding or groundwater.

Moist soils found throughout the riverbottom during low flows were ideal places for cottonwood and willow trees to sprout. These saplings matured into cottonwood forests that were important to the river's ecosystem. In the forest's understory grew hackberries, oaks and other hardwoods that would eventually replace the cottonwoods. The mixed vegetation in the Missouri River Valley - woodlands, grasslands and wetlands - served the needs of many species of resident and migratory wildlife. The constant lateral movement of the river maintained a natural succession.

Fish that adapted to the Missouri's turbid waters included the shovelnose and pallid sturgeons, paddlefish, catfish and sauger. Flooding in the spring filled the river with nutrients that served as the base of the food chain. Many fish species took rising or falling water levels as cues to spawn, as did insects that the fish fed upon. Some species spawned in the floodplain when the river left its banks. When the river subsided, slack water areas below sandbars and in side channels and backwaters provided ideal nursery habitat for young fish, and as primary habitat for small species such as the plains minnow. Trees consumed by the river during high flows dotted the riverbed, offering habitat for aquatic insects that were another key food-chain component. Largemouth bass, bluegills, crappies and other fish filled the oxbow lakes. On September 1, 1804, Clark wrote in his journal, "number of Cat fish caught, those fish so plenty that we catch them at any time and place in the river."

Work to tame the Missouri River, or at least make it manageable, began soon after the first steamboats began to ply its waters in the early-1800s. The U.S. Army Corps of Engineers began removing snags to improve steamboat navigation. In the late-1800s, the Corps attempted to stabilize the river's banks in places, but with little success. In the early-1900s, Congress authorized the Corps to build a six-foot navigation channel from Kansas City to St. Louis. That project stalled, but resumed in 1927 when Congress provided funds and called for the six-foot channel to be extended to Sioux City, Iowa.

Pile dikes were driven across much of the Missouri's width, forcing its water into a narrow, deep, self-scouring channel. Side channels and backwaters were cut off from the river. Slowed by these dikes, the river dropped its sediment behind them, creating new land that became forest and in most locations was later cleared and farmed. In Nebraska, these accretion areas became property of adjacent landowners. Iowa kept it as public land.

The first dam on the main stem of the Missouri River, Fort Peck Dam in Montana, was built under President Franklin D. Roosevelt's Works Progress Administration and finished in 1937. Calls for more flood control in lower basin states followed floods in 1943 and led Congress the next year to pass the Flood Control Act, which included the Pick-Sloan Missouri Basin Program.

This project would build five more dams, primarily for flood control and to support navigation below Sioux City. But it would provide jobs for soldiers when they returned from World War II,

Wayne Werkmeister of the National Park Service inspects an illegal bank stabilization project on the unchannelized Missouri River near Wynot. Such projects inhibit natural erosion processes and reduce the scenic value of the river.

too. The project would supply water to 4.7 million acres of farmland and generate hydropower, both of which were expected to expand settlement in the arid upper-basin states. Only 10 percent of the irrigation project was developed. Fish, wildlife and recreation were also to benefit.

Construction of the dams - Garrison in North Dakota, Oahe, Big Bend and Fort Randall in South Dakota and Gavins Point in Nebraska - was completed in 1963. Combined, the six dams can store 74 million acre-feet of water. The resulting reservoirs inundated 1.6 million acres of bottomland, displacing, among others, thousands of Native Americans, many of whom had been moved to reservations along the river less than 100 years earlier.

A nine-foot navigation channel from Sioux City to the river's mouth was completed in 1981. Once a mile wide or more, the river now spans only 600 feet through most of Nebraska. To improve navigation, the river was straightened. The lake at DeSoto National Wildlife Refuge near Blair is one result of that effort. In all, the work cut 205 miles from the river's length in 1895.

Below Sioux City, the Missouri River's floodplain covers 1.9 million acres. An estimated 168,000 acres of aquatic habitat and 354,000 acres of adjacent riverine habitat were lost to channelization and the development that followed. Nearly 20 percent of the combined losses were in Nebraska.

For about 385 miles, the Missouri serves as Nebraska's northern and eastern border. It has many different faces in that length, most with problems that detract from the river's value as fish and wildlife habitat.

The water released from Fort Randall Dam a few miles from Nebraska's northern border flows cold and clear. For 39 miles to Niobrara, the Missouri retains some of its natural characteristics, including islands, side channels, sandbars and backwaters. This reach was designated a National Recreational River by Congress in 1991.

But this stretch and two others in Nebraska suffer from insufficient sediment. Before 1950, the river annually carried an average of 142 million tons of sediment past Sioux City. It now carries just four million tons. The rest is trapped in the upstream reservoirs. Clean water continually scours the riverbed deeper, greatly incising its channel.

Flows from Fort Randall Dam are highly regulated, varying slightly each day to meet hydropower demands, and seasonally, to provide high flows during the navigation season and low flows in winter. The clear water supports sight-feeding fish such as walleyes, but native river fishes are few. This segment is cut off from the rest of the river by two dams, preventing fish from moving up or downstream.

Gene Zuerlein, a Commission fisheries biologist and leader on Missouri River issues, said the cold water released from the depths of the reservoirs disrupts natural cues aquatic insects use to reproduce or hatch. "All of those insects are in sync," Zuerlein said. "They're part of the food base, so if they're out of sync, that means the food may not be available for the fish at the right time."

At the mouth of the Niobrara River, the Missouri changes. The Niobrara dumps 1,400 acre-feet of sediment into the Missouri each year, enough to cover a football field a quarter-mile deep. That is more than half of the sediment deposited annually in Lewis and Clark Lake a few miles downstream. The sediment has formed a delta at the upper end of the reservoir, which has lost more than 20 percent of its original 575,000 acre-foot capacity, and according to Corps estimates will be completely filled with sediment by 2175. Between the mouth of the Niobrara and the lake, the riverbed is aggrading, or rising. This has raised the local water table, forcing relocation of the village of Niobrara and Niobrara State Park from the floodplain to higher ground, and requiring roads to be raised.

From Gavins Point Dam to Ponca State Park, the river again appears natural, meandering through the countryside, with a few islands and sandbars. This 59-mile segment was designated a National Recreational River in 1978. But it faces problems similar to the reach below Fort Randall Dam. Channel incision has lowered the bed by as much as 14 feet. As the last dam in the system, Gavins Point releases water to support navigation. Its flows are steady and vary seasonally.

Bank stabilization is a significant problem in this unchannelized reach. Wayne Werkmeister of the National Park Service, which manages national recreational rivers, said between 17 to 35 percent of the river bank in this stretch has been stabilized with rock, concrete rubble, cinder blocks, tires, and even concrete, which has been poured down banks.

The Wild and Scenic Rivers Act generally prohibits bank stabilization on designated rivers, Werkmeister said. The Corps, however, was granted authority for demonstration stabilization

A Missouri River sandbar formed below a chevron built in 2002 by the U.S. Army Corps of Engineers at Hamburg Bend near Nebraska City is exposed by low winter river flows. The Corps also reduced the height of a wing dike to allow the river to carve at its bank, increase the top-width of the river and create shallow-water habitat.

projects in the late-1970s and has maintained them since by adding more rock. "When you start looking at it, it dawns on you that all they're doing here is connecting the dots [between stabilized areas]," he said.

Landowners along the river also stabilize the banks to prevent the river from claiming their cabins or farms, which sit only a few feet above the river. Such projects are required by law to be approved by the Corps, but many are not. Recent violations include a landowner who dumped concrete rubble over the bank to limit erosion on his mile of shoreline.

The Park Service is working with the Corps to resolve this problem, which reduces needed sediment in the river and reduces its scenic value.

The bank stabilization and navigation project that was part of Pick-Sloan begins below Ponca State Park, where the mile-wide river is funneled into a channel 600 feet wide. Incision is a problem between Sioux City and the mouth of the Platte River, lowering the riverbed 10 feet or more.

In the three incised stretches, the water table has fallen. Wetlands in the floodplain that historically were filled when water overflowed the banks or were maintained by groundwater are now dry. Many have been filled in and are now farmed.

From the mouth of the Platte River to the southern Nebraska border and beyond, the channel is aggrading, or rising, thanks to heavy inflows of sand and soil contributed by the Platte. A levee system, originally proposed to run along the entire channelized reach to protect much of the bottomland from flooding, follows the river downstream from Omaha. When the river comes out of its banks during periodic high flows, vegetation along the river filters out sediment. This has raised the land between the levees, and filled wetlands.

There is little shallow, slow-moving water in the channelized reach. Some is formed in eddies below wing dikes. But the river in this stretch resembles a canal, with swift flows from bank to bank and little variation in depth. Catfish are still caught there, but their numbers have been greatly reduced. Other native fish are rare. A Commission study in 1994 found a 70 to 98 percent decline in several chub and minnow species native to the Missouri River in Nebraska.

The Corps of Engineers is working to restore some riverine habitat that was lost to channelization. The Missouri River Fish and Wildlife Mitigation Project is the primary tool. Approved by Congress in the 1986 Water Resources Development Act and expanded in 1999, it authorizes the Corps to acquire private land from willing sellers in the floodplain and restore

Just out of its egg, an interior least tern chick lies next to its yet-to-be-hatched sibling in a nest on a Missouri River sandbar.

aquatic and terrestrial habitat on that land and existing public land. If fully funded, 166,750 acres could be improved in the next 30 years, including 27,000 acres in Nebraska. Six projects in Nebraska, five of which are complete, include constructed chutes and backwaters and will provide more than 7,150 acres of public land. On those projects, however, only 250 acres of new aquatic habitat were created.

The USFWS contends more acres are needed. It has recommended the Corps create 20 to 30 acres of shallow water habitat per river mile and create sandbars in the channel.

The Corps is working on such a project between Hamburg Bend, near Nebraska City, and Peru. It is lowering the wing dikes on inside river bends, which will allow water to flow over the dikes rather than around them, and erode the adjacent publicly owned land. This process will create holes, sandbars and shallow water in the river and increase its surface width. The Corps also is installing chevrons, structures that will cause sandbars to form below them. These projects are designed so they will not hinder navigation.

Zuerlein said, "That's what the river needs. It needs to be able to wiggle a little bit versus being chained down."

This work and current and future mitigation projects will restore some of the river's natural form. But in its biological opinion, the USFWS said the Corps must also restore function - including changes in flows - to give native species a chance to recover. A spring rise would provide spawning cues for fish, rebuild or maintain sandbar habitat and enhance aquatic habitat by connecting the river to side channels and backwaters. Low summer flows would ensure that tern and plover nests on the sandbars would not be flooded and also enhance fish productivity.

The National Academy of Sciences, which in 2002 released findings of its study of the Missouri River system, agreed with the USFWS. "Degradation of the Missouri River ecosystem will continue unless some portion of the hydrologic and geomorphic processes that sustained the preregulation Missouri River and floodplain ecosystem are restored - including flow pulses that emulate the natural hydrograph and cut-and-fill alluviation associated with river meandering," the Academy's report stated.

In the revision of its Master Manual, the Corps proposed four alternatives that included a spring rise from May through mid-June, conducted every three years on average, that would increase flows from Gavins Point Dam 40 to 60 percent more than normal. Lower summer flows from mid-June through August each year would cut flows by 30 to 40 percent. Opposition to change was been intense, and the issue has become a political football that is still being kicked around.

Despite assurances that a spring rise would not occur during years when tributary runoff is high, many fear that a rise will cause flooding in lower basin states, keeping farmers out of their fields during planting season. Scientists said the fears are unfounded. For each tributary that joins the Missouri, releases from Gavins Point Dam become a smaller percentage of total river flows. Downstream, large tributary inflows are the main cause of flooding.

Robert Jacobsen, a research hydrologist with the U.S. Geological Survey in Columbia, Missouri, modeled the Missouri River's flows for the Corps alternatives based on daily flows for the past 100 years. For the model that calls for the highest spring rise and lowest summer low - a plan

The natural Missouri River, shown here looking downstream toward Ponca State Park, provides a diverse mix of terrestrial and aquatic habitat. The amount of open sandbar habitat needed for nesting least terns and piping plovers on this bend has declined.

recommended by the Commission and others - "there's little change" below the mouth of the Platte River, Jacobsen said. "[At Nebraska City] the spring rise would be very similar to what's going on now. The big difference would be in the summer low, when there would be an appreciable time from July to September when flows would be less than the current water control plan and also less than the minimum navigation levels."

Some farmers are concerned about interior drainage problems caused by higher river flows in the areas protected by levees. In these areas, streams flow through the levees when the Missouri's levels are normal. When the river is high, gates are closed so water doesn't back up into the bottomland. Pump stations operated by drainage districts move water from creeks over the levees and into the river.

Allan Adams is the fourth generation to farm bottomland near Peru. His son, Brett, is the fifth. He thinks the Corps has underestimated the damage that can be caused when a heavy rain falls while the river is high. "You can only pump so much," he said. If pumps can't keep up, water can back up and flood fields miles from the river. Closer to the river, groundwater seepage can make fields too wet to plant even before the river reaches flood stage. Farmers and drainage districts developed the land under the assumption that river management would stay the same. Adams said changing things now would be "like changing the rules of a ballgame in the seventh inning."

He added, "The reason they want to do all of this is to save two birds and a fish. Well those two birds and a fish, they're not game birds or a game fish. They're not really good for anything in our point of view."

Navigation interests are opposed to lower summer flows that could require a split navigation season, something they say would break the industry. The Corps estimates the $7 million in economic benefits provided by navigation would be reduced by up to $2 million under the proposed changes. Randy Asbury of the Coalition to Protect the Missouri River, a group representing agricultural and commercial interests, said the Corps estimates are well off the mark and that the mere presence of barge traffic forces railroads to "be more efficient and competitive." This, he said, helps support grain prices.

But those backing changes on the river point out that barge traffic has not met expectations, and the cost of maintaining the navigation channel exceeds the benefits. Projected by the Corps to reach 5 million tons by 1980, commercial traffic peaked at 3.3 million tons in 1977. In 2000, it totaled only 1.3 million tons. Less than a third was grain, according to an Iowa State University study. Most commercial traffic, the study said, is fertilizer brought upriver in the spring and grain shipped downriver in the fall, a schedule that fits with a split navigation season that low summer flows might require.

The National Academy of Sciences report said the Corps Master Manual is "a self-imposed limitation on its discretion" and that the agency is not bound by law to provide a navigation season or flows outlined within the manual. The Academy even suggested the Corps do an incremental analysis of the economic benefits provided to each segment of the river, compared to the amount spent to maintain it. Most commercial barge traffic is in Missouri, and traffic progressively decreases between there and Sioux City. If it were shown that costs outweighed benefits above Omaha, Nebraska City or even Kansas City, it would allow more habitat restoration in those reaches, "changes that would compromise, but not necessarily eliminate, navigational uses," the report stated.

The USFWS said the Corps was to implement flow changes by 2003. The Corps was on pace to meet that deadline until July 2002, when President George W. Bush supported a five-year delay.

In response, a coalition of 10 environmental groups, including American Rivers, took the Corps to court in February, arguing its management of the Missouri violated the Endangered Species Act. A prolonged drought that had drawn reservoirs to nearly historical lows ruled out a spring rise in 2003. But environmental groups and upstream states, which were concerned about low reservoir levels, still wanted the Corps to reduce summer flows. Supported by the state of Missouri, the Corps planned to continue its water releases to maintain navigation. In Nebraska, the opinions on reduced summer flows were split: the Game and Parks Commission backed low flows while others, including the attorney general and governor, backed higher flows. Upstream states sued to keep water in their reservoirs.

The issue bounced between courts, and judges issued conflicting rulings. In August, the Corps complied with one ruling and lowered flows for three days ending August 15, a date chosen to

Boaters stop to play on a Missouri River sandbar north of Omaha in August. With normal summer flows, most sandbars are under water.

coincide with the end of the tern and plover nesting seasons. Municipalities along the river expressed fears that flows would drop river levels below their water intake pipes. Power plants, which draw cooling water from the river, feared they would have to cut production. Marina operators feared boaters would not be able to get through channels that led from docks to the river. Others feared it would halt all recreational boating on the river.

"What's happened over time, because of the way the Missouri River is managed, is people have almost come to think of it as a lake," said Chad Smith, director of American Rivers' Nebraska field office. "And it's not a lake. It's a river and people need to understand that water levels go up and down on a river."

The lower flows in August 2003 were a test under difficult conditions - a drought that reduced inflows. But, of all the fears, there were few adverse effects. The city of Omaha closed one marina to protect its docks and some large boats had difficulty getting in and out of other marinas. The Commission contends those issues can be resolved. Boat ramps on the river were functional.

"What it shows is that in the real world, if you can break through all of the rhetoric, teeth gnashing and hand wringing, the bottom line is that we can make these modest flow changes, do better things for the river and life goes on," said Smith.

With normal releases, water levels in the channelized reach run high on the river's steep banks, giving boaters few places to stop. River levels last summer were lower than normal because of drought and the reduced releases. These lower flows exposed sandbars below wing dikes, providing boaters, sunbathers and picnickers room to roam.

"This gives the kids a place to play," said Susie Ledger of Omaha, as her children played and swam in the shallow water next to a sandbar north of Omaha where her family beached their boat the first Sunday in August.

A week later, when flows dropped further to meet the court order, even more sandbars were exposed, especially between Gavins Point Dam and Ponca State Park. It is there that flow changes will provide the most benefits to least terns and piping plovers.

Summer releases from Fort Randall and Gavins Point dams were higher than normal from 1995 through 1997. The releases were double the norm in 1997, but less than what is proposed for a spring rise. The high flows rebuilt sandbars in the unchannelized reaches and scoured them of vegetation. With ideal habitat, average production of both terns and plovers from 1998 to 2001 increased by more than 200 percent in those reaches when compared to the averages for 1986 to 1994.

Corps biologists monitoring nests between Montana and Ponca have documented record production for four years straight, in part because of habitat created in 1997, and in part because of drought. Greg Pavelka, who monitors tern and plover nests on the river in northern Nebraska, said 829 of the 1,338 adult plovers nesting throughout the Missouri this year used the shoreline exposed by falling water levels at Lake Sakakawea and Lake Oahe. Pavelka said 51 of the birds nested in the reach between Fort Randall Dam and Lewis and Clark Lake, where there had been almost no activity before the high flows. Another 286 plovers nested between Gavins Point Dam and Ponca.

Production in that reach has remained high for longer than expected, Pavelka said. "We expected, at most, four to five years of good production, and now we've had six years," he said. But the river has eroded more than 40 percent of the 3,016 acres of sandbars available in 1998, and vegetation has covered 80 percent of what remains, forcing the birds to concentrate in a few open areas. Production fell in the same reach for the endangered tern, which requires more riverine habitat than plovers. Considering 366 of the 741 terns nesting on the system did so in that 59-mile reach, continued decline in habitat there does not bode well for the species.

For fish, the first mitigation project completed in Nebraska, a flow-through chute at Hamburg Bend, demonstrated what habitat and high flows could provide. In 1997, the river left its banks and covered the entire bend, scouring the newly reopened chute as well as other areas. Sampling by

Commission fisheries biologists sample fish in the channelized Missouri River near Peru. The number of native fish have declined in the river. Future studies will document how fish respond to changes in river habitat and flows.

Commission biologists found increased production of native chubs and minnows following the wet period. But the river has not been out of its banks since, and populations have quickly declined. "Habitat alone is not enough to sustain the positive responses," said Gerald Mestl, a Commission fisheries biologist working on Missouri River programs. "But if you build the habitat and get the flows, you will get the response."

Those years also showed what high flows can do for terrestrial habitat along the river. New growth of cottonwoods and willows, which had for the most part ceased throughout the Missouri River, was found in many areas. And some new wetlands were scoured in the floodplain between the levees.

In restoring habitat along the Missouri, other states have focused on creating terrestrial habitat. For many years the Commission's guiding philosophy in restoration has focused on creating aquatic habitat. "You start with aquatic habitat and the other habitats will follow," said Scott Luedtke, a Commission wildlife biologist who works on river habitat projects.

According to Corps estimates, recreation provided $87 million in economic benefits in 1994. About three-fourths of those benefits are realized in the upper basin states, primarily in the large reservoirs in the Dakotas and Montana. Those states want their interests placed on equal footing with navigation and want the barge industry to share more of the pain in drought years. South Dakota Game, Fish and Parks estimated receding water levels at Lake Oahe in 2003 would cost the state's economy $9.6 million. Similar losses were expected in North Dakota, which saw Lake Oahe recede from its borders for the second time and watched Lake Sakakawea approach record lows.

Zuerlein believes a healthier river in the channelized reaches will provide more economic and recreational benefits, too. More than 40 percent of Nebraska's population lives in counties that border the river, and studies have shown a need for more water-based recreation opportunities in eastern Nebraska. Lower flows will make the river more inviting to smaller craft. Zuerlein pointed out that in a restored river, fish and wildlife populations will increase, leading to more fishing, hunting and wildlife watching opportunities.

Through the mitigation project, the decision has already been made to restore habitat. Resolving the flow issue will not be the last difficult decision to make for the river. For example, biologists believe more sediment should move through Lewis and Clark Lake, where it causes problems, to the reach below Gavins Point Dam, where it is needed. The Corps has considered several options, including a bypass, dredging and even building a canal to move the mouth of the Niobrara below the dam, but no solution is now seen as feasible. Another possibility is draining Lewis and Clark Lake and then using Fort Randall Dam to create a flood pulse to flush sediment through Gavins Point Dam. The flows required to make the process worthwhile might cause flooding along the river below both dams. It could flush most of the game fish through the system as well, ruining two quality fisheries that exist in the river above the reservoir and reservoir itself. But, if nothing is done the reservoir will eventually disappear, along with its fishing and boating.

If nothing is done to restore the health of the Missouri's ecosystem, more than the least tern, piping plover and pallid sturgeon could disappear. In all, 82 species of fish, birds, plants, reptiles, mammals, insects and mussels native to the Missouri are now rare, threatened or endangered. "Current operations, if continued without significant alterations, likely will cause further declines in other native species and likely will result in additional species being listed as threatened or endangered," the USFWS said in its biological opinion.

The Corps, in its proposed Master Manual revision, suggested incorporating adaptive management in its operations. The philosophy calls for the testing of theories, monitoring of the tests and basing management decisions on what is learned. The National Academy of Sciences report recommends the Corps abandon its Master Manual revision and move ahead solely under the guiding principal of adaptive management. The manual can then be revised when more questions have been answered.

The Academy's report said a stakeholders group should be formed to form consensus- and science-based river management decisions. It said Congress should enact legislation that would facilitate recovery of the river ecosystem, including authority for the Corps to compensate those adversely affected by changes in dam operations.

"They're basically saying 'Let's set up some experiments and try a few different things and acknowledge we're not going to know everything about everything immediately,' " Zuerlein said. "So you do things on an incremental basis. You try it and if it works, you do more."

No matter what decisions are made regarding the future of the river, the Corps will likely find itself in court. The legal battles could take as long or longer than the process to revise the Master Manual, which the Corps said should be finished this year. Any decision will have negative effects on someone or something somewhere along the river. But so does continuing to operate the river as is.

"If we wait until we know everything there is to know about the Missouri River, the world will have come and gone," Zuerlein said. "We need to change because the opportunity to do a lot of different things is there. We know what the problems are, let's fix them."