1
Introduction

Rivers, watersheds and aquatic ecosystems are the biological engines of the planet.

World Commission on Dams, 2000

The Missouri River basin (Figure 1.1) extends over 530,000 square miles and covers approximately one-sixth of the continental United States. The one-hundredth meridian, the boundary between the arid western states and the more humid states in the eastern United States, crosses the middle of the basin. The Missouri River’s source streams are in the Bitterroot Mountains of northwestern Wyoming and southwestern Montana. The Missouri River begins at Three Forks, Montana, where the Gallatin, Jefferson, and Madison rivers merge on a low, alluvial plain. From there, the river flows to the east and southeast to its confluence with the Mississippi River just above St. Louis. Near the end of the nineteenth century, the Missouri River’s length was measured at 2,546 miles (MRC, 1895). Large, looping meanders of the main channel, some of which were nearly circular and that measured tens of miles in circumference, were then prominent features of the river. Much of the river has since been dammed, straightened, and channelized, and these large meanders have been virtually eliminated. As a result, the Missouri River’s length today is 2,341 miles—a shortening of roughly 200 miles (USACE, 2001).

Between 1804 and 1806, Meriwether Lewis and William Clark led the first recorded upstream expedition from the river’s mouth at St. Louis to the Three Forks of the Missouri, and eventually reached the Pacific coast via the Columbia River. The Missouri River subsequently became a corridor for exploration, settlement, and commerce in the nineteenth and early twentieth centuries, as navigation extended upstream from St. Louis to Fort Benton, Montana. Social values and goals in the Missouri River basin in



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The Missouri River Ecosystem: Exploring the Prospects for Recovery 1 Introduction Rivers, watersheds and aquatic ecosystems are the biological engines of the planet. World Commission on Dams, 2000 The Missouri River basin (Figure 1.1) extends over 530,000 square miles and covers approximately one-sixth of the continental United States. The one-hundredth meridian, the boundary between the arid western states and the more humid states in the eastern United States, crosses the middle of the basin. The Missouri River’s source streams are in the Bitterroot Mountains of northwestern Wyoming and southwestern Montana. The Missouri River begins at Three Forks, Montana, where the Gallatin, Jefferson, and Madison rivers merge on a low, alluvial plain. From there, the river flows to the east and southeast to its confluence with the Mississippi River just above St. Louis. Near the end of the nineteenth century, the Missouri River’s length was measured at 2,546 miles (MRC, 1895). Large, looping meanders of the main channel, some of which were nearly circular and that measured tens of miles in circumference, were then prominent features of the river. Much of the river has since been dammed, straightened, and channelized, and these large meanders have been virtually eliminated. As a result, the Missouri River’s length today is 2,341 miles—a shortening of roughly 200 miles (USACE, 2001). Between 1804 and 1806, Meriwether Lewis and William Clark led the first recorded upstream expedition from the river’s mouth at St. Louis to the Three Forks of the Missouri, and eventually reached the Pacific coast via the Columbia River. The Missouri River subsequently became a corridor for exploration, settlement, and commerce in the nineteenth and early twentieth centuries, as navigation extended upstream from St. Louis to Fort Benton, Montana. Social values and goals in the Missouri River basin in

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The Missouri River Ecosystem: Exploring the Prospects for Recovery FIGURE 1.1 The Missouri River Basin. SOURCE: USACE, undated. this period reflected national trends and the preferences of basin inhabitants. Statehood, federalism, and regional demands to develop and control the river produced a physical and institutional setting that generated demands from a wide range of interests. Over time, demands for the benefits from the Missouri’s control and management resulted in significant physical and hydrologic modifications to the river. These modifications led to substantial changes in the river and floodplain ecosystem. Numerous reservoirs are scattered across the basin, with seven large dams and reservoirs located on the river’s mainstem. Six of these dams were constructed pursuant to a 1944 agreement between the U.S. Army Corps of Engineers and the Department of the Interior’s Bureau of Reclamation. The agreement, ratified by the U.S. Congress, is known as the Pick–Sloan Plan and is the effective existing management regime for the Missouri River. The Pick–Sloan Plan represented a merger of Missouri River basin development plans that were formulated independently in the early 1940s by the Corps of Engineers (the Corps’ “Pick Plan” was headed by Colonel Lewis A. Pick) and the Bureau of Reclamation (the Bureau’s “Sloan Plan” was headed by Regional Director William G. Sloan). The separate plans were coordinated in Senate Document 247 (S.D. 247), which

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The Missouri River Ecosystem: Exploring the Prospects for Recovery was part of the Flood Control Act passed by Congress on December 22, 1944. The final paragraph of S.D. 247 states that the plan “will secure the maximum benefits for flood control, irrigation, navigation, power, domestic, industrial and sanitary water supply, wildlife, and recreation.” The first public mainstem dam on the Missouri River pre-dated Pick– Sloan. The Fort Peck Dam was built in Montana in the 1930s as a Works Progress Administration project promoted by President Franklin D. Roosevelt. The five mainstem dams downstream of Fort Peck and dozens of tributary dams were constructed as part of Pick–Sloan. Missouri River mainstem reservoirs behind Fort Peck Dam in Montana (Fort Peck Lake), Garrison Dam in North Dakota (Lake Sakakawea), and Oahe Dam in South Dakota (Lake Oahe) are three of the nation’s five largest human-made lakes (only Lake Mead and Lake Powell, both on the Colorado River, are larger). Although the river and its tributaries are extensively controlled by dams, channel modifications, and bank stabilization projects, the Missouri River is still subject to flooding, especially on the lower river. Like most major U.S. water projects, the Missouri River dams were authorized and built prior to the passage of modern environmental statutes such as the National Environmental Policy Act (1969) and the Endangered Species Act (1973), but not the Fish and Wildlife Coordination Act of 1934, which predates most of the dams. The Corps of Engineers constructed and operates six of the Missouri’s seven mainstem dams (the Bureau of Reclamation constructed and operates Canyon Ferry dam, the comparatively small mainstem dam farthest upstream). Operations of these six dams are guided by the Corps’ 1979 Missouri River Main Stem Reservoir System Reservoir Regulation Manual, usually referred to as the “Master Manual.” A severe drought across the basin in the late 1980s and early 1990s focused national attention on the tensions and conflicts among management objectives and competing beneficiaries. During this drought, upper basin reservoirs were drawn down (reducing benefits for recreation and tourism), and lower basin states experienced disruptions to navigation and water supplies. The pronounced drought of 1988–1992 affected most parts of the Missouri River basin. Negative impacts on reservoir-based recreation (upstream), on navigation (downstream), and on threatened and endangered species were so severe that in 1989, Congress directed the Corps to review the Master Manual. That review was conducted according to guidelines in the National Environmental Policy Act (NEPA), which requires the Corps to conduct an environmental impact statement (EIS) regarding changes in dam operations. As early as August 1994, the U.S. Fish and Wildlife Service (USFWS) issued jeopardy opinions (which state that a proposed action will jeopardize the existence of a threatened or endangered species) regarding operation of the Missouri River dams and the threat to federally

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The Missouri River Ecosystem: Exploring the Prospects for Recovery listed species (the Fish and Wildlife Service opinions were issued as part of the environmental impact study process). This followed the Corps’ issuance of the Master Manual Draft Environmental Impact Statement, which recommended changes in the management of the dams and reservoirs. The Corps conducted public hearings on this draft document. These hearings revealed controversies and passionately-held beliefs surrounding the river’s many users. A consensus emerged that recognized the need for improved ecological monitoring and scientific knowledge to improve river management. Nevertheless, the National Environmental Policy Act environmental impact statement process—initiated when the Corps began revisions to its Master Manual in 1989—and a final revision of the Corps’ Master Manual for operation of the Missouri River system had not been completed in early 2002, nearly 14 years after the Master Manual revision process began. Congress, the Missouri River basin states, and the basin’s water users and interest groups disagree on the appropriate water release schedule (including timing, locations, and quantities of water) for the Missouri River’s mainstem reservoirs. In 1999, with sponsorship of the U.S. Environmental Protection Agency (EPA) and the Corps of Engineers, the Water Science and Technology Board of the National Research Council (NRC) formed a committee of experts to help provide a better scientific basis for river management decisions in the Missouri River basin. This study complements similar NRC studies of the Columbia River basin, the Colorado River basin, the Florida Everglades, and the Upper Mississippi River. It also recognizes a growing public interest in redressing modifications made to large river ecosystems. This committee was given the following charge: This committee will provide a general characterization of the historical and current status, and important ecological trends, of the Missouri River and floodplain ecosystem. The committee will provide a review of the available scientific information on the Missouri River and floodplain ecosystem, and will identify and prioritize scientific information needs for improved Missouri River management. The committee will also recommend policies and institutional arrangements that could improve scientific knowledge of the Missouri River and floodplain ecosystem, and those that could promote adaptive management of the Missouri River and flood-plain ecosystem. The committee’s task was thus divided into three objectives: 1) Characterize the historical and current ecological status of the Missouri River and floodplain ecosystem. This overview will identify key ecological conditions, changes, and processes, endangered and threatened species, trends and relevant time scales, and gaps in and the limits of that knowledge.

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The Missouri River Ecosystem: Exploring the Prospects for Recovery 2) Identify and describe the general state of existing scientific information on the Missouri River and floodplain ecosystem. Identify and prioritize the key scientific questions to be addressed and the key scientific information needed for improved Missouri River management. 3) Recommend policies and institutional arrangements for improving Missouri River and floodplain ecosystem monitoring and research, and those that could promote an adaptive management approach to Missouri River and floodplain ecosystem management. This committee began its two-year study late in 1999. Five meetings were held along the river: Bismarck, North Dakota; Columbia, Missouri; Great Falls, Montana; Omaha, Nebraska; and Pierre, South Dakota (a sixth meeting was held at the National Academies’ Beckman Center in Irvine, California, in February 2001). The committee spoke with federal and state scientists and engineers, representatives from Indian tribes, experts on Missouri River institutions and policies, groups interested in Missouri River ecology and river management, the commercial navigation industry, and many citizens. This report focuses on the Missouri River ecosystem. However, an understanding of the larger context of water resources development is helpful in explaining some of the patterns reflected across the Missouri basin. Namely, changing values and water management policies in the United States are part of a larger global shift in which assumptions about the benefits of dams and the ability to appropriately distribute those benefits are being rethought. ECOLOGICAL CONDITIONS AND TRENDS IN U.S. RIVERS The rivers of the United States underwent considerable hydrologic and ecological changes during the twentieth century. The most obvious of these changes was the inundation of extensive stretches of these rivers behind dams. The twentieth century saw the Corps of Engineers and the Bureau of Reclamation, along with local, state, and private entities, construct hundreds of dams and greatly increase water storage. For example, in a given year, 60 percent of the United States’ entire river flow can be stored behind dams (Hirsch et al., 1990). Dams in the Missouri River basin have the capacity to hold roughly 106 million acre-feet of water, with the six Corps of Engineers Missouri mainstem reservoirs having a combined capacity of roughly 73.4 million acre-feet, making it North America’s largest reservoir system (USACE, 2001). The waters stored by these reservoirs are intended to serve multiple purposes, including irrigation, recreation, and controlled releases for navigation enhancement. The reservoirs are also operated so

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The Missouri River Ecosystem: Exploring the Prospects for Recovery that flood-control storage is available, an amount that fluctuates through the year in response to snowpack and precipitation conditions in the basin. Major hydrologic changes in some sections of the Missouri River attended the closures of the Corps’ mainstem Missouri dams: Fort Peck in 1937, Fort Randall in 1952, Garrison in 1953, Gavins Point in 1955, Oahe Dam in 1958, and Big Bend Dam in 1963. When they were constructed, the Missouri River mainstem dams were intended to help control river flows and to reduce streamflow variability. Today, however, there is a better understanding of and appreciation for the ecological values and services supported by streamflow variability (Box 1.1 describes the values of ecosystem goods and services). Decreases in riverine wetlands and other riparian (streamside) habitats in U.S. river systems have resulted from population growth and economic development, as well as from structural alterations (e.g., straightening of channels, bank stabilization, and construction of wing dams) designed to constrict flows to a main channel. A variety of indicators might be used to measure changes in these ecosystems. To use one example, a National Research Council committee estimated that total wetland acreage in the contiguous United States decreased by approximately 117 million acres— half the original total—by the mid-1980s (NRC, 1995). Another study found that two-thirds of the pre-European settlement areas of riparian vegetation in the United States have been replaced by other land uses (Moberly and Sheets, 1993). Regardless of the measure chosen, U.S. riparian ecosystems have been greatly altered during the past century. Human impacts on U.S. rivers have reduced populations of many aquatic species, including some extinctions. In the Columbia River basin, Pacific salmon have disappeared from about 40 percent of their historical breeding ranges over the past century (NRC, 1996). In the Upper Mississippi–Illinois River system, the number of mussel species has declined by 23 percent to 44 percent since European settlement in the nineteenth century (USGS, 1999). Only four of eight endemic fishes remain in the Grand Canyon reach of the Colorado River, and some of these are threatened or endangered (Minckley, 1991). Engineered changes in the nation’s rivers have enhanced competition, predation, and other detrimental interactions between native and nonnative species (Minckley and Deacon, 1991), which has contributed to the demise of native species. Missouri River reservoirs and river segments presently contain populations of exotic fishes, including cisco, several salmon and trout species, and several Asian carp species (Hesse et al., 1989). Some of these species have contributed to the development of economically important recreational fisheries. On the Upper Mississippi River, scientists reported increased abundance of species such as bluegill and largemouth

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The Missouri River Ecosystem: Exploring the Prospects for Recovery Box 1.1 Ecosystem Goods and Services Although knowledge of the importance of ecosystems to societies and economies dates back centuries, discussion of nature’s importance in terms of goods and services is a relatively recent phenomenon. Because many functions provided by ecosystems are not monetized and are not traded in markets, values are often under-appreciated by the public and by decision makers (Daily, 1997). For example, clean air and clean water provided by ecosystems are fundamental to healthy societies and economies, but price tags are generally not affixed to air and fresh-water systems. They thus may be treated as having no monetary value in market-based decisions. But if rational natural resources decisions are to be made, it is important to understand how ecosystems provide value to societies and the magnitude of those values. Ecosystem goods and services include fish protein, fish-based recreation, biomass fuels, wild game, timber, clean air and water, medicines, species richness, maintenance of soil fertility, and natural recharge of groundwater. Consistent with the fact that ecosystem goods and services are generally not priced, are not traded in markets, and are not owned, they tend to become needlessly scarce. To remedy this, conservation programs that protect fish and wildlife are enacted, parks and natural reserves are created, the use of the biosphere as a sink for wastes is regulated, and programs aimed at restoring natural habitat are mandated. A variety of approaches are in use to correct for the unowned and unpriced nature of many ecosystem goods and services. Tradable rights or quotas have been introduced for certain pollutants and in some fisheries. Charges are levied by governments to prevent the overuse of certain goods and services. Several methods are used to place simulated market values on goods and services that would otherwise be unpriced in policy making or in court decisions. bass, which colonized habitats with slow-moving (lentic) water, after the river’s navigation dams were constructed (Fremling and Claflin, 1984). SHIFTING VALUES AND PUBLIC PREFERENCES Large, regional water projects no longer enjoy the widespread political support they once did. The economic rationale for these projects has eroded and there is today more concern over these projects’ environmental and social costs. As a result, the arid and semiarid western United States is shifting from the reclamation era—characterized by the construction of large, federally subsidized regional water projects—to an era of reallocation, conservation, and ecosystem restoration. The Bureau of Reclamation today focuses on management and maintenance of existing projects and on ecological improvements in degraded stream systems. Similarly, the Corps of Engineers is faced with the challenge of carrying out engineering and construction activities while balancing competing social, environmental,

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The Missouri River Ecosystem: Exploring the Prospects for Recovery and economic demands in highly developed and highly controlled river systems. The Corps’ traditional roles have been expanded by Congress to include environmental restoration and programs that address environmental problems associated with existing projects. For example, the Corps plays a central role in the multi-billion dollar Florida Everglades restoration project. The value of dams today is questioned by segments of society that value environmental preservation and enjoyment. Some smaller U.S. dams have been breached or removed (e.g., Edwards Dam on the Kennebec River in Maine was breached in 1999), and others are scheduled to be removed (e.g., Elwha Dam in the state of Washington). In addition, the possible removal or decommissioning of some large federal dams (e.g., four dams on the lower Snake River and Hetch Hetchy Dam in Yosemite National Park) has been discussed (ASCE, 1997; Gleick, 2000). During the 1980s and 1990s, Congress passed specific legislation aimed at protecting and/or restoring aquatic ecosystems in the Columbia River basin, the Florida Everglades, the Grand Canyon, and the San Francisco Bay Delta. The need to consider the conditions under which dams and hydroelectric power facilities should be retired has also drawn attention from professional engineering groups (ASCE, 1997). Changing views toward large dams are reflected in the recent report of the World Commission on Dams (WCD, 2000). In 1997, the World Bank and the International Union for the Conservation of Nature and Natural Resources (The World Conservation Union) assembled a group to discuss the highly controversial issues associated with dams. These parties agreed to a proposal to work together to establish a World Commission on Dams (WCD), which in 1998 began a comprehensive global and independent review of the performance and impacts of large dams. The commission’s final report was issued in 2000 (WCD, 2000). Although care must be taken in applying findings from the commission’s global review of dams to the Missouri River, many of the commission’s findings regarding environment, indigenous people, equity, and sustainability are applicable to the Missouri River basin and to the United States. This committee reviewed the commission’s report with interest and, where its findings are relevant, refers to this report. ADAPTIVE MANAGEMENT To properly balance social, economic, and environmental considerations in large river ecosystems, organizations and management policies must be able to respond to and take advantage of changing environmental, social, and economic conditions, as well as address extreme events. The concept of adaptive management promotes the notion that management

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The Missouri River Ecosystem: Exploring the Prospects for Recovery policies should be flexible and should incorporate new information as it becomes available. New management actions should build upon the results of previous experiments in an iterative process. It stresses the continuous use of scientific information and monitoring to help organizations and policies change appropriately to achieve specific environmental and social objectives. Adaptive management promotes collaborative and consensus-based decision-making. Adaptive management promotes “thinking outside the box” and stakeholder discussions about the desired state of the ecosystem. Responsive organizations and policies that can adjust decisions on dam operations are needed to meet changing scientific and social goals: “Dams and the context in which they operate are not seen as static over time. . . . Management and operation practices must adapt continuously to changing circumstances over the project’s life and must address outstanding social issues” (WCD, 2000). Adaptive management requires an organizational and political framework for its full and proper implementation. To be successful, it should be implemented by organizations with sufficient legal authority and political legitimacy to appropriately adjust management policies. Scientific investigations will never eliminate all economic, engineering, environmental, and social uncertainties in large ecosystems like the Missouri River basin. Policy decisions must account for these uncertainties. Organizations responsible for promoting adaptive management must have the legal authority and the stakeholder support necessary to make and enforce recommended changes in current management regimes. Adaptive management also promotes the advancement of scientific knowledge through carefully designed experiments and monitoring systems. Water resources managers and scientists across the United States are conducting numerous experiments, at a range of spatial and temporal scales, with water releases and diversions to benefit select species and ecosystems. Perhaps the most prominent experiments in river and dam management are controlled releases of high flows from reservoirs. The most famous controlled release in United States water management was a controlled flood from Glen Canyon Dam in March 1996. The controlled flood in the Grand Canyon aimed to restore beaches that had been damaged by decades of low hydrologic variability. The notion of operating a dam to purposely create a large flood represented a milestone in U.S. water management. Former Secretary of the Interior Bruce Babbitt described the event and the process leading up to it: “There was simply no precedent on the Colorado River—or as far as we know anywhere in the history of civilization—for what Interior was proposing to do” (Babbitt, 1999). Beyond reservoir releases, possible adaptive management actions for the Missouri River in-

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The Missouri River Ecosystem: Exploring the Prospects for Recovery clude changing the length of navigation seasons, changing patterns of irrigation water withdrawals, changing elevations of navigation pools, and constructing notches in flood-control levees. This committee studied carefully the history of efforts to create coordinated management schemes for the Missouri River basin through federal river authorities modeled on the Tennessee Valley Authority (TVA), through interstate compacts, and through an entity composed of federal, state, and tribal representatives. In general, the proposed organizations lacked the necessary political support to achieve agreement on implementation and have thereby been unable to resolve most intra-basin conflicts. The lack of such a management authority in the Missouri River basin has created a management vacuum that has been filled by the Corps and increasingly by the courts (Thorson, 1994). If adaptive management is chosen as a paradigm by which to coordinate Missouri River management organizations and policies, it must be considered and implemented in the context of these current and historical organizational efforts. It would require Congress, federal and state agencies, Indian tribes, and other public and private stake-holders to forge an agreement placing adaptive management at the center of a process for reaching compromises on the full array of river management issues. This committee addressed its charge against a backdrop of over a century of actions devoted to developing and managing the Missouri River for economic and social ends. Before evaluating contemporary Missouri River management issues, a review of the historical development of the Missouri River and its floodplain is appropriate.