Executive Summary

Over the past century, human activities have caused substantial ecological changes to the Missouri River ecosystem. By any measure, the Missouri River ecosystem—the Missouri River’s main channel and its flood-plain—has experienced significant reductions in natural habitat and in the abundance of native species and communities. There have also been substantial reductions in the daily and annual variability of hydrologic and geomorphic processes. Causes of these changes include the removal of snags from the river in the late 1800s; introduction of nonnative fish species beginning in the late 1800s; navigation enhancement beginning in the early 1900s; and damming and flow regulation of the mainstem Missouri River beginning in the 1930s. Land use changes (including urbanization, agriculture, transportation infrastructure) and population growth have also affected the ecosystem in less direct but important ways.

River systems have often proved remarkably resilient, withstanding a variety of human modifications and still responding positively to ecosystem restoration efforts. Strategies for improving ecological conditions in large river systems are relatively new, but some smaller rivers have exhibited rapid and positive ecological responses. In the Kissimmee River in Florida, for example, plant communities, fish, and invertebrates responded favorably to water-level manipulation experiments in the early 1980s. More recently, the breaching of Edwards Dam on Maine’s Kennebec River in 1999 resulted in increases in the abundance of select bird and fish species. Nonetheless, there is a point beyond which a large, degraded river system



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The Missouri River Ecosystem: Exploring the Prospects for Recovery Executive Summary Over the past century, human activities have caused substantial ecological changes to the Missouri River ecosystem. By any measure, the Missouri River ecosystem—the Missouri River’s main channel and its flood-plain—has experienced significant reductions in natural habitat and in the abundance of native species and communities. There have also been substantial reductions in the daily and annual variability of hydrologic and geomorphic processes. Causes of these changes include the removal of snags from the river in the late 1800s; introduction of nonnative fish species beginning in the late 1800s; navigation enhancement beginning in the early 1900s; and damming and flow regulation of the mainstem Missouri River beginning in the 1930s. Land use changes (including urbanization, agriculture, transportation infrastructure) and population growth have also affected the ecosystem in less direct but important ways. River systems have often proved remarkably resilient, withstanding a variety of human modifications and still responding positively to ecosystem restoration efforts. Strategies for improving ecological conditions in large river systems are relatively new, but some smaller rivers have exhibited rapid and positive ecological responses. In the Kissimmee River in Florida, for example, plant communities, fish, and invertebrates responded favorably to water-level manipulation experiments in the early 1980s. More recently, the breaching of Edwards Dam on Maine’s Kennebec River in 1999 resulted in increases in the abundance of select bird and fish species. Nonetheless, there is a point beyond which a large, degraded river system

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The Missouri River Ecosystem: Exploring the Prospects for Recovery can only be recovered with costly remediation efforts. Some losses—such as species extinction—can never be restored. Given the size and complexity of the Missouri River ecosystem, it is not clear where the point of irreparable environmental change lies, or how close the Missouri River ecosystem might be to passing that point. However, the following changes in the Missouri River ecosystem jeopardize its fundamental natural processes: the loss of natural flood pulses; the loss of natural low flows; straightening of stream meanders and the elimination of cut-and-fill alluviation; losses of natural riparian vegetation; reductions in water temperature variation; introduction of nonnative species; and extensive bank stabilization and stream channelization. Specific examples of twentieth century changes in the Missouri River ecosystem include the following: Nearly 3 million acres of natural riverine and floodplain habitat (bluff to bluff along the Missouri River’s mainstem) have been altered through land-use changes, inundation, channelization, and levee building. Sediment transport, which was the hallmark of the pre-regulation Missouri River (and was thus nicknamed “The Big Muddy”), has been dramatically reduced. Sediment transport and deposition were critical to maintaining the river system’s form and dynamics. For example, before the 1950s, the Missouri River carried an average of roughly 142 million tons of sediment per year past Sioux City, Iowa; after closure of the dams, an average of roughly 4 million tons per year moved past the same location. Damming and channelization have occurred on most of the Missouri River basin’s numerous tributary streams, where at least 75 dams have been constructed. The amplitude and the frequency of the Missouri River’s natural peak flows have been sharply reduced. With the occasional exception of downstream sections in the state of Missouri, the Missouri River no longer experiences natural spring and summer rises and ecologically-beneficial low flows at other times of the year. Cropland expansion and reservoir impoundment have caused reductions in natural vegetation communities. These vegetation communities continue to shrink with the additional clearing of floodplain lands. The remaining remnant areas will be critical in any efforts to repopulate the floodplain ecosystem. Reproduction of cottonwoods, historically the most abundant and ecologically important species on the river’s extensive floodplain, has largely ceased along the Missouri River, except in downstream reaches that were flooded in the 1990s and in upstream reaches above the large dams. Production of benthic invertebrates (e.g., species of caddisfly and mayfly) has been reduced by approximately 70 percent in remnant unchannelized river reaches. Benthic invertebrates are an important food

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The Missouri River Ecosystem: Exploring the Prospects for Recovery source for the river’s native fishes and an important component of the river’s food web. Of the 67 native fish species living along the mainstem, 51 are now listed as rare, uncommon, and/or decreasing across all or part of their ranges. One of these fishes (pallid sturgeon) and two avian species (least tern and piping plover) are on the federal Endangered Species List. In many reaches of the river, nonnative sport fishes exist in greater abundance than native fish species. The nonnative fishes are often more tolerant of altered conditions of temperature, turbidity, and habitat. Although some nonnative fish produce substantial economic benefits, nonnative species may also contribute to the declining abundance of native fish. These ecosystem changes are not merely abstract, scientific measurements; they also represent the loss of valued goods and services to society. Examples of ecosystem goods and services include outdoor recreation, biomass fuels, wild game, timber, clean air and water, medicines, species richness, maintenance of soil fertility, and the natural recharge of groundwater. It is often difficult to recognize the economic values that are lost with declines of these ecosystem benefits, largely because they have historically not been carefully measured. But ecosystem-based activities often provide important economic benefits. For example, thousands of people enjoy canoeing on the Missouri River in Montana each year, which provides an important source of tourism-based income. The values of many of these services historically have not been monetized and are not traded in economic markets. Changes in the benefits flowing from these services are thus not easily recognized. With the exception of select outdoor recreation activities, most ecosystem goods and services tend to be undervalued by decision makers and in resources management policies. But there is a growing recognition that the replacement costs of these services, assuming their replacement is even possible, would be very high. Degradation of the natural Missouri River ecosystem is clear and is continuing. Large amounts of habitat have been transformed in order to enhance social benefits, and the ecosystem has experienced a substantial reduction in biological productivity as a result. Natural riverine processes, critical to providing ecosystem goods and services, have been greatly altered. The ecosystem has been simplified and its production of goods and services has been greatly compromised. Degradation of the Missouri River ecosystem will continue unless some portion of the hydrologic and geomorphic processes that sustained the pre-regulation Missouri River and floodplain ecosystem are restored—including flow pulses that emulate the natural hydrograph, and cut-and-fill

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The Missouri River Ecosystem: Exploring the Prospects for Recovery alluviation associated with river meandering. The ecosystem also faces the prospect of irreversible extinction of species. STATE OF THE SCIENCE There is a rich, extensive body of scientific research on the Missouri River ecosystem that can provide the foundation for future river management actions. For example, a 1997 technical report from the U.S. Geological Survey listed 2,232 studies of the Missouri River ecosystem. These scientific studies date back to Lewis and Clark’s epic 1804–1806 expedition. Since then, many individuals and government agencies have studied the basin’s natural vegetation, fishes, water quality, and impacts of dams. This research has greatly improved scientific understanding of the river’s ecosystem and how it has changed. These studies have provided careful documentation of the ecological changes described in this report. Research on the Missouri River ecosystem provides a sound scientific understanding of ecological structure and the controlling river processes, and how they were impacted by human actions during the twentieth century. Although knowledge of the ecological intricacies within a system as large as the Missouri River ecosystem will always be limited by scientific uncertainties, the system’s broad ecological parameters and patterns are currently well understood. Nonetheless, existing studies are only a starting point for future management choices because this extensive body of research has not been adequately synthesized. Further, the studies have tended to focus on specific species or portions of the river. Only a few studies of Missouri River ecology view the river as a single system from headwater to mouth, or as a single system that considers biological and physical linkages. The lack of synthesis and utilization of these scientific data may be as much a function of institutional and political barriers as it is of the limitations of the scientific information itself. Neither discrete scientific disciplines nor mission agencies have been provided with sufficient incentives to conduct this synthesis and integration. Without this fundamental information, cast within a system-wide perspective encompassing the entire Missouri River ecosystem, truly comprehensive assessments of the ecological state of the Missouri River are not possible. The most significant scientific unknowns in the Missouri River ecosystem are how the ecosystem will respond to management actions designed to improve ecological conditions. In addition to improving ecological conditions, such actions can also help supplement existing scientific knowledge, especially in understanding how select ecological variables respond to different environmental conditions. Management actions, cast as carefully circumscribed and monitored experiments, are necessary in order to ad-

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The Missouri River Ecosystem: Exploring the Prospects for Recovery vance our understanding of how regulated rivers respond to changes. It is important that ecosystem monitoring programs be designed specifically to produce results that serve as input into river ecosystem recovery programs. The emerging paradigm of adaptive management provides a useful conceptual basis for framing such management actions. The concept has been and is currently being used to guide ecosystem restoration efforts in the Colorado River, the Columbia River, and the Florida Everglades. Adaptive management is also being initiated by Missouri River management agencies. The U.S. Army Corps of Engineers, for example, in its August 2001 revised draft environmental impact statement for the Missouri River Master Water Control Manual, acknowledges the importance of adaptive management. This committee was requested to comment on “policies and institutional arrangements . . . that could promote an adaptive management approach to Missouri River and floodplain ecosystem management.” Adaptive management recognizes that scientific uncertainties and unforeseen environmental changes are inevitable. It thus seeks to design organizations and policies that can adapt to and benefit from those changes. Adaptive management is not merely an elaborate “trial and error” approach. Rather, it emphasizes the use of carefully designed and monitored experiments, based on input from scientists, managers, and citizens, as opportunities to maintain or restore ecological resilience and to learn more about ecosystems. These actions are monitored for scientific findings to help improve understanding of how policy decisions affect ecosystems. Findings from ecosystem monitoring are then to be used to appropriately adjust management policies. Adaptive management requires that clear goals and desired outcomes be established so that progress toward desired future conditions can be assured. Although adaptive management is a powerful approach that holds great potential, it should not be viewed as a panacea for Missouri River basin management and ecosystem improvements. The committee was keenly aware that the practice of adaptive management is “a work in progress” and that there is inadequate experience with successful or unsuccessful experiments to comprehensively evaluate the underlying theory. Adaptive management is not necessarily easy to implement and execute and, like the Missouri River basin itself, presents many complexities. In those ecosystems where it has been implemented, it has proven useful in many ways. However, endangered species are still listed, stakeholders still disagree with one another, and key management agencies are constrained by resources, legal mandates, and political realities. Nonetheless, there can be little disagreement that a new management paradigm is needed if further declines in the Missouri River ecosystem are to be halted and reversed. Adaptive management represents a framework for promoting stakeholder discussion

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The Missouri River Ecosystem: Exploring the Prospects for Recovery and for strengthening the links between the Missouri River ecosystem and the region’s economies and societies. Just as adaptive management encourages experiments, implementation of adaptive management will in itself represent an experiment. But no other alternative restoration strategy holds the promise that adaptive management does, and federal, state, and local governments, as well as several other National Research Council committees, have embraced the concept as an important instrument to promote biodiversity conservation and restoration. The U.S. Army Corps of Engineers, in cooperation with the U.S. Fish and Wildlife Service and several state agencies, has completed and is implementing several habitat preservation and restoration projects along the Missouri River. These projects represent useful steps toward recovering the Missouri River ecosystem. However, they are limited in scope, are insufficiently coordinated among agencies and among various reaches of the river, receive inconsistent funding, and lack adequate support for monitoring. These programs also are not framed within an overarching plan for recovering key elements of the Missouri River’s pre-regulation hydrologic and geological processes. The sum of these efforts is insufficient to noticeably recover ecological communities and fundamental physical processes in the Missouri River ecosystem. To substantially improve the ecosystem, a more systematic and better-coordinated approach that considers ecological conditions on par with other management goals in the entire Missouri River system will be required. MISSOURI RIVER NAVIGATION AND BANK STABILIZATION No Missouri River management issue has polarized the river’s stakeholders as much as the debate over how the provision of flows and channel depths for navigation has affected the Corps’ ability and willingness to meet ecosystem needs. Improved navigation was a major feature of the mid-twentieth century vision of the 1944 Pick–Sloan Plan, as navigation’s future economic benefits were assumed to be substantial. However, the 1950 projections for commercial waterway traffic were overly optimistic; commercial towboat traffic on the Missouri River peaked in 1977 (below projected levels) and has fallen slowly and steadily since then. Missouri River navigation, conducted on the river’s 735-mile channelized stretch between Sioux City, Iowa and St. Louis, Missouri, is controversial for both economic and environmental reasons. The current dam and reservoir operation schedules reduce the river’s natural hydrologic variability in order to provide a steady and reliable 9-foot deep navigation channel. Such operations run counter to established river science, in which a large degree of natural hydrological variability is essential to biological

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The Missouri River Ecosystem: Exploring the Prospects for Recovery productivity and species richness of large floodplain rivers. A resolution of the differences between managing flows for navigation or for more natural hydrology is constrained by the fact that the benefits of navigation are expressed in dollars, while the benefits of ecosystem improvements from operational changes have yet to be monetized. The ultimate decision regarding the proper balance between these uses is a public policy issue and, as such, was beyond this committee’s charge. Nevertheless, this issue is so crucial to the river’s future that this committee could not ignore it. Differences of opinion may be artificially magnified by framing Missouri River navigation as an “all or nothing” issue. Cooperative dialogue might be easier if incremental changes in navigation and river management were considered. Because net national navigation benefits are relatively small in total, and because waterway traffic volumes decrease moving upstream, an incremental analysis of the economics of retaining segments of the navigable waterway would be useful. Relaxing the responsibility to maintain navigation flows would make it demonstrably easier to introduce flows for improving river ecology in that segment. As an example, if the segment from Sioux City, Iowa downstream to Omaha, Nebraska proved to be uneconomic when comparing its incremental benefits with its incremental costs— factoring in the values of all potential ecosystem goods and services—then that segment would be a candidate for enhancing river ecology through operational changes. Ecological enhancement, however, would not necessarily proceed rapidly. The banks along the river’s navigable channel are stabilized and contain communities and other important infrastructure in many areas. If it is decided to enact management actions to improve the state of the ecosystem, and if those management actions are to be effective, some degree of Missouri River meandering must be restored. Allowing the Missouri River to meander would require a significantly wider public corridor in some portions of the channel than currently exists. This would require close coordination with those who live and work along the river. In some cases, significant improvements in river ecology may require relocations. In proceeding segment by segment, the analysis should discover the point at which it is beneficial to retain navigation to the mouth of the river. The case for retaining some navigation might be stronger if navigation were discontinued or less fully supported in those segments where it is economically inefficient. Congress should give the Corps of Engineers authority to provide navigation services on an incremental basis along the channelized portion of the Missouri River, to be exercised on the basis of analysis and stakeholder input.

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The Missouri River Ecosystem: Exploring the Prospects for Recovery POLICIES, INSTITUTIONS, AND ADAPTIVE MANAGEMENT The Corps of Engineers constructed and operates six of the seven mainstem dams on the Missouri River; the U.S. Bureau of Reclamation operates the seventh, Canyon Ferry Dam, east of Helena, Montana. When the Corps of Engineers constructed five of the Missouri River mainstem dams in the 1950s and 1960s after passage of the Pick–Sloan Plan, goals for dam and reservoir operations were to reduce flood damages, enhance navigation, generate hydroelectric power, and store water for irrigation. But changes in social preferences have resulted in a new mix of uses and stakeholders on the Missouri River today. Many of these new uses revolve around recreational and environmental considerations, such as boating and sport fishing. Some Missouri River stakeholders, such as environmental and recreational groups, call for revised operations and a redistribution of the river’s benefits. Other stakeholders, such as the navigation industry, the hydropower industry, and floodplain farmers generally prefer the status quo. Scientific knowledge, economies, and social preferences have clearly changed across the Missouri River basin since the mainstem dams were planned and constructed. However, the institutional and policymaking framework for Missouri River management has not changed accordingly. The decision-making context for the Missouri and its tributaries is characterized by prolonged disputes, disaffected stakeholders, and degrading ecological conditions. Barriers to resolving this policy gridlock on the Missouri River include a lack of clearly stated, consensus-based, measurable management objectives, powerful stakeholders’ expectations of a steady delivery of entitlements, and sharply differing opinions and perspectives among some Missouri River basin states. Current management protocols for operating the Missouri River system represent an accretion of federal laws, congressional committee language, appropriations instructions, and organizational interpretations that have been enacted or developed over the past century. This guidance has generally not been updated to reflect changing economic and social conditions, new needs in the basin or the nation, or advances in scientific knowledge. The Corps of Engineers and some basin stakeholders view the collective statutes, committee reports, and agency interpretations as barriers to prospective management changes that would seek to balance ecological values and services with current realities and values of navigation, recreation, and sound floodplain management. Although this committee believes the Corps of Engineers may have greater legal authority to manage the Missouri River system than it has exercised, the Corps’ ability to do so has been constrained by sharp differences of opinion among stakeholders. If the condition of the Missouri River ecosystem is to improve, agencies

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The Missouri River Ecosystem: Exploring the Prospects for Recovery responsible for adaptive management must have clear lines of authority and the necessary resources to work toward this goal. The Corps of Engineers has always set the water release schedules for the Missouri River mainstem dams. Guidance for mainstem dam water release priorities is established in the Corps’ Missouri River Main Stem Reservoir System Reservoir Regulation Manual, also known as the “Master Manual.” Decisions regarding water release schedules from the Missouri River mainstem reservoirs ultimately determine the distribution of the river’s benefits. As mentioned, these decisions have become increasingly controversial and pose challenges to the Corps. In the late 1980s, the Corps of Engineers began a revision to its 1979 Master Manual that today—thirteen years later—is not yet complete because of competing demands for the river’s resources and sometimes strong differences of opinion. In working toward this revision, the Corps has consulted with numerous stakeholders and the public at large across the Missouri basin, including environmental groups, the navigation industry, farmers, and other floodplain residents and communities. Any agency would be challenged to find a solution amenable to all users in the current context of Missouri River management, and a consensus on how the dams and reservoirs are to be operated has remained elusive. A moratorium on further revision of the Master Manual should thus be implemented until such revisions reflect a collaborative, science-based approach based upon adaptive management to improve the condition of the Missouri River ecosystem. Adaptive management should be adopted as an ecosystem management paradigm and decision-making framework for modifying water resources and reservoir management for the Missouri River ecosystem. As part of this management strategy, the goal of improving ecological conditions should be considered on par with other management goals. Specific Missouri River adaptive management experiments and activities—involving a broad spectrum of river system stakeholders in a collaborative process to establish goals and guidelines for such experiments—should be implemented as soon as possible. Adaptive management actions for improving ecological conditions should be examined and conducted within a systems framework that considers the entire Missouri River ecosystem from headwaters to mouth, as well as the effects of tributary streams on the mainstem. Determining specific goals and objectives for Missouri River management that society desires will require the participation of a wide spectrum of groups with stakes in Missouri River management. Missouri River mainstem reservoir operations objectives and means, including adaptive management actions, should be set by a formal multiple-stakeholder group that includes, but is not necessarily limited to, the U.S. Army Corps of Engineers, the U.S. Department of Energy, the U.S. Environmental Protec-

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The Missouri River Ecosystem: Exploring the Prospects for Recovery tion Agency, the U.S. Fish and Wildlife Service, the U.S. National Park Service, Indian tribes, the Missouri River basin states, floodplain farmers, navigation groups, municipalities, and environmental and recreational groups. The stakeholder group should review other adaptive management efforts to learn about successes, failures, and potential management actions that could be usefully implemented on the Missouri. To help resolve scientific uncertainties and to assure progress in considering some level of ecosystem recovery, a scientific peer-review process that includes an independent, interdisciplinary scientific panel should provide solicited input to the stakeholder group. Support of the U.S. Congress is ultimately needed to help establish acceptable goals for the use and management of the Missouri River system. Congress must also identify the necessary authorities to do so. The stakeholder group should help frame Missouri River management decisions. But if the trends of ecosystem decline are to be halted and reversed, that stakeholder group must define ecosystem improvements as one of its key goals. Federal legislation mandating ecosystem protection and enhancement is one means to help stakeholders focus on Missouri River ecology. Sustained stakeholder participation in a system the size of the Missouri River ecosystem, and in which there are sharp differences of opinion over appropriate management goals, will require sustained commitments of time and resources. Some of the participants may possess inadequate resources and will require assistance to ensure their participation. Successful implementation of adaptive management will also require administrative and facilitation resources. Congress should provide the necessary legislative authorities and the fiscal resources to implement and sustain an adaptive management approach to Missouri River management. Resources should include administrative and facilitation services for a multiple-stakeholder group to develop consensus positions on river management objectives and reservoir operations policies. To ensure support of the adaptive management program and management actions that balance contemporary social, economic, and environmental needs in the Missouri basin, Congress should enact a federal Missouri River Protection and Recovery Act designed to improve ecological conditions in the Missouri River ecosystem. This act should include a requirement for periodic, independent review of progress toward implementing adaptive management of the Missouri River ecosystem.