3
Missouri River Governance: Institutions, Laws, and Policies for Managing Sediment and Related Resources

As discussed in Chapter 2, many of the major changes to Missouri River hydrology and sediment can be traced back to the middle of the twentieth century. Specifically, the 1944 Flood Control Act authorized the Pick-Sloan Plan and the 1945 Rivers and Harbors Act authorized the Missouri River Bank Stabilization and Navigation Project (BSNP). The goals of these projects were to reduce floods; provide a reliable channel for commercial navigation; generate hydroelectric power; help provide water for communities along the river; and provide jobs for servicemen returning to the United States after World War II. The Pick-Sloan legislation included two other goals important to future management of Missouri River resources: recreation, and fish and wildlife protection. These uses over time would frequently come into conflict with the dominant interests of hydropower, water supply, navigation, and flood control. It is important to recognize that Pick-Sloan was more than an engineering infrastructure program and included authorizations for various river and reservoir system management objectives.

The lines of authority for constructing and operating these projects were relatively clear. The Corps of Engineers, under its flood control and navigation enhancement responsibilities, had extensive authority under the Pick-Sloan Plan and the BSNP. Congress assigned authority for Pick-Sloan dam construction to the Corps of Engineers. The Corps constructed hundreds of miles of revetments and levees along the river under the BSNP and also was in charge of post-construction operations and maintenance of these structures. In the years immediately after passage of Pick-Sloan and



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3 Missouri River Governance: Institutions, Laws, and Policies for Managing Sediment and Related Resources A s discussed in Chapter 2, many of the major changes to Missouri River hydrology and sediment can be traced back to the middle of the twentieth century. Specifically, the 1944 Flood Control Act authorized the Pick-Sloan Plan and the 1945 Rivers and Harbors Act autho- rized the Missouri River Bank Stabilization and Navigation Project (BSNP). The goals of these projects were to reduce floods; provide a reliable chan- nel for commercial navigation; generate hydroelectric power; help provide water for communities along the river; and provide jobs for servicemen returning to the United States after World War II. The Pick-Sloan legisla- tion included two other goals important to future management of Missouri River resources: recreation, and fish and wildlife protection. These uses over time would frequently come into conflict with the dominant interests of hydropower, water supply, navigation, and flood control. It is important to recognize that Pick-Sloan was more than an engineering infrastructure program and included authorizations for various river and reservoir system management objectives. The lines of authority for constructing and operating these projects were relatively clear. The Corps of Engineers, under its flood control and navigation enhancement responsibilities, had extensive authority under the Pick-Sloan Plan and the BSNP. Congress assigned authority for Pick- Sloan dam construction to the Corps of Engineers. The Corps constructed hundreds of miles of revetments and levees along the river under the BSNP and also was in charge of post-construction operations and maintenance of these structures. In the years immediately after passage of Pick-Sloan and 51

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52 MiSSOuRi RivER PlANNiNg the BSNP, the Corps played a dominant role in Missouri River decision making. With changes in laws and shifts in social preferences and priorities, the setting of decision-making processes for Missouri River management has become more complicated. Notable changes in the legal setting include passage of the National Environmental Policy Act (NEPA) in 1969, the Clean Water Act (CWA) in 1972, the Endangered Species Act (ESA) in 1973, and several other environmental protection statutes. Along with this new federal legislation, recreational uses of the river were an authorized purpose of the Pick-Sloan Plan, and slackwater recreation in the lakes cre- ated by the dams is accorded a high priority today by many citizens. For the Corps of Engineers, this means operating the system to meet demands of all six authorized uses—flood control, water supply, hydropower, com- mercial navigation, recreation, and fish and wildlife. Examples of these latter interests include water-based recreation on the National Wild and Scenic River segments in Montana and on the National Recreational River segments in Nebraska and South Dakota, which were developed in response to the National Wild and Scenic Rivers Act of 1968. Moreover, under the Endangered Species Act the Corps must comply with legal requirements to protect federally listed native species from extinction as a consequence of their actions and recover and maintain their populations by removing or lessening threats of their actions to the species’ survival. Additionally, under the 1934 Fish and Wildlife Coordination Act, federal agencies were required to mitigate for habitat loss due to water development projects. The 1934 act was specifically applied to the Missouri River under the 1980 Fish and Wildlife Coordination Act Report and became the origin of the Mis- souri River Mitigation Program (described later in this chapter). Congress expects Corps of Engineers dam and reservoir system opera- tions to reflect these multiple goals. In that regard the Missouri River Mas- ter Water Control Manual (Master Manual) was prepared by the Corps in 1960. The most recent Master Manual update was released in March 2006, after consultation with user groups and government agencies across the basin. The change was motivated by the desire to meet authorized purposes and newly emerging demands on the system, but more importantly to be in compliance with the 2000/03 U.S. Fish and Wildlife Service Biological Opinion. Today, decisions about how to manage the river’s dams, reservoirs, navi- gation channel, and other resources are guided by an extensive body of laws, agency guidance documents, budgets, and river users who can voice their preferences through the political process. In some instances conflicts among users and among agencies with conflicting missions are resolved through court rulings. This report refers to the collective body of these interrelated laws and policies as the “governance system” for Missouri River management.

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53 MiSSOuRi RivER gOvERNANCE This chapter describes the current governance system, how it has changed and become more complicated over time, and the challenges this presents today to the Corps and other parties. Consistent with this report’s statement of task, its focus is on sediment-related issues. In many ways the Corps remains the focal point of Missouri River management; but as this chapter describes, its authority to make decisions is now shared with others, especially the U.S. Fish and Wildlife Service. This chapter provides background for understanding Missouri River governance that is discussed later in the report. In doing so, it describes relevant laws, institutions, and policies for managing Missouri River sediment and related resources. It also provides advice relevant to Question 7 in the report’s statement of task regarding improved management strategies. MISSOURI RIVER MANAGEMENT, THE CORPS OF ENGINEERS, AND SHARED DECISION MAKING The process of submitting management plans for review by others is not new to the Corps of Engineers. Nevertheless, the influence of that review process on Corps decision making has increased over time. This chapter highlights the many laws, organizations, and manuals that guide and govern Corps of Engineers decision making, beginning with one of the earliest requirements—compliance with the Fish and Wildlife Coor- dination Act. Fish and Wildlife Coordination Act Passed in 1934 and amended in 1946, 1958, 1978, and 1995, the Fish and Wildlife Coordination Act (or the “Coordination Act”) was designed to promote preservation and enhancement of fish and wildlife by requir- ing equal consideration of their habitat needs in conjunction with federal participation in water resource development. The act authorizes the U.S. Fish and Wildlife Service (FWS) to make recommendations for modifica- tions in project design or operation to benefit fish and wildlife resources. Federal agencies like the Corps must give full consideration to the FWS recommendations, as well as any recommendations made by the agency exercising administration over the wildlife resources of the affected state. The Coordination Act also specifies that water development project plans include such justifiable measures for wildlife conservation, as determined by water management agencies, to obtain maximum overall project benefits. Thus, as a procedural requirement, the Corps must receive and fully con- sider recommendations from the FWS and state wildlife agencies; however, acceptance of the recommendations is at the discretion of the Corps. This is not to suggest that the Coordination Act has had limited influ-

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54 MiSSOuRi RivER PlANNiNg ence. In fact, the earliest efforts to address habitat losses associated with river development, especially the BSNP, were initiated as a result of the act. In the early 1980s the Fish and Wildlife Service, executing its com- ment responsibilities under the Coordination Act, reported that the BSNP had significantly reduced fish and wildlife habitat, caused fish and wildlife population declines, and the loss of recreational opportunities (USFWS, 1980). In order to mitigate these effects, the Congress directed a Corps study that resulted in the 1984 report, “Missouri River Bank Stabilization and Navigation Project, Final Feasibility Report and Final EIS for the Fish and Wildlife Mitigation Plan.” The Missouri River Mitigation Plan was subsequently authorized under the Water Resources Development Acts of 1986 (Public Law 99-662) and expanded in 1999 (Public Law 106-53). The primary activity under the mitigation plan is acquiring land from will- ing sellers and then developing aquatic and terrestrial habitat throughout the project’s length by dredging filled-in areas, reopening historical chutes, bank stabilization, dike notching, pumping, dike/levee construction, and vegetative plantings. The Mitigation Project plan calls for the development of 166,750 acres of land in separate locations along the river in Nebraska, Iowa, Kansas, and Missouri. The Corps began implementing the mitigation plan in 1991. As of September 2009, 56,606 acres of Missouri River flood- plain land have been acquired from willing sellers within the four states. Total costs, including land acquisition, planning, engineering and design, habitat development, construction management, operation and mainte- nance during construction, and monitoring, totaled $132,792,000 through 2006 (USACE, 2007). The mitigation plan continues and has become an integral part of the larger Missouri River Recovery Program (MRRP), or additional programs being carried out or planned under new authorities, such as the Missouri River Ecosystem Restoration Program (MRERP) that was authorized under WRDA 2007 (see below). Wild and Scenic Rivers Act The Wild and Scenic Rivers Act mandates preservation of the “out- standingly remarkable scenic, recreational, geologic, fish and wildlife, his- toric, cultural, or other similar values” of free-flowing, designated rivers. River segments can be designated as wild, scenic, or recreational. Congress declared its intent to protect the natural features of the Missouri River by designating several river segments under this Act. In the upper reaches of the river in Montana, a 64-mile segment below Fort Benton, Montana, has been designated as wild and another 85 miles as scenic or recreational. Further downstream, a 39-mile segment from Fort Randall Dam to Lewis and Clark Lake, which straddles South Dakota and Nebraska, has been designated as a recreational river. Additionally, a 59-mile river segment

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55 MiSSOuRi RivER gOvERNANCE downstream from Gavins Point Dam also has been designated as a rec- reational river. Together, these segments comprise significant portions of the remaining unimpounded river in the upper basin, and their islands, sandbars, chutes, and snags that retain some of the river’s former dynamic character. National Environmental Policy Act The National Environmental Policy Act (NEPA) was enacted in 1969. The act required all federal agencies, including the Corps, to prepare analy- ses that assess and report on proposals for major federal actions with sig- nificant environmental impacts. The NEPA process provides a significant mechanism for information sharing, public involvement and comment by other agencies of governments at all levels. In passing this act, Congress ex- pected that no federal agency decision would be made without a thorough understanding of environmental impacts and alternatives. The National Environmental Policy Act thus demands attention to its procedural require- ments to gather, receive, and consider advice on the effects of a range of reasonable alternatives to the proposed federal action. The act does not, however, dictate which alternative the agency must choose, and it does not require the federal action agency to act upon the advice of other agencies or the public. The National Environmental Policy Act and the Coordina- tion Act are similar in that the Corps must solicit input, and must consider carefully the information received, but need only take it into consideration when making decisions. Yet, like the Coordination Act, the NEPA process can have great influ- ence on the decision made. As discussed in greater detail below, revisions made to the Corps operations of the dam and reservoir system and as de- scribed in the so-called Master Manual, required an environmental impact statement. The processes and procedures required by NEPA created both a forum for debate and for public and interagency review and comment on technical analyses. The Corps’ Record of Decision, which explains the basis for its decision to adopt the Master Manual, includes commitments to future actions that have since been implemented and that do govern the way the Corps manages the river, including habitat creation actions that go beyond those included in the Missouri River Mitigation Plan. Endangered Species Act The federal Endangered Species Act (ESA), passed in 1973, puts respon- sibility on federal action agencies to comply with, not just consider, recom- mendations of federal wildlife agencies to minimize or avoid the impact of federal activities on endangered species. Also, the U.S. Fish and Wildlife

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56 MiSSOuRi RivER PlANNiNg Service may specify steps that need to be taken to recover populations of a species when the FSW demonstrates that past activities of the action agency contributed to the species decline. The process by which this decision is made and then agreed to by the FWS and the affected federal agency (in this instance the Corps) follows a well-defined set of steps. Under Section 4 of the Endangered Species Act, the U.S. Department of the Interior (or Department of Commerce) is authorized to list species as endangered or threatened and to designate critical habitat. Once a spe- cies is listed, no person may “take” the species by killing it or otherwise harming it, and no federal agency may take an action that jeopardizes the continued existence of the endangered species or that modifies its criti- cal habitat. Moreover, the federal agency must consult with the Fish and Wildlife Service, then must demonstrate to the satisfaction of the Fish and Wildlife Service that the proposed actions will not jeopardize the continued existence of the species or adversely modify its critical habitat. If the Fish and Wildlife Service issues a finding of jeopardy in its biological opinion, it will recommend reasonable and prudent alternatives (RPAs) designed to accomplish the objectives of the action in question without causing jeop- ardy. Federal regulations define a reasonable and prudent alternative as an action that (1) can be implemented in a manner consistent with the intended purpose of the action; (2) can be implemented consistent with the scope of the action agency’s legal authority and jurisdiction; (3) is economically and technologically feasible; and (4) would, the Fish and Wildlife Service believes, avoid the likelihood of jeopardizing the continued existence of listed species or resulting in destruction or adverse modification of critical habitat (see Code of Federal Regulations (CFR) Title 50, Section 402.02). A decision to deviate from reasonable and prudent alternatives recom- mended by the Fish and Wildlife Service will not in and of itself violate the Endangered Species Act, but it may expose the action agency to the risk of penalties or injunctive relief in the event that a court finds a violation of the jeopardy prohibition. Clearly the Endangered Species Act is different from the Coordination Act not only in focus, but also in the way it allows the Fish and Wildlife Service to place conditions on the Corps’ exercise of its congressional authorities to operate the Missouri River dam and reservoirs system. This is one way in which the decision making on Missouri River management today has broadened. A biological opinion issued by the Fish and Wildlife Service in 2000 under authority granted by the Endangered Species Act, along with a supplemental opinion in 2003, has directed Corps of Engineers habitat construction plans and other activities along the Missouri River—especially downstream of Gavins Point Dam.

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57 MiSSOuRi RivER gOvERNANCE Fish and Wildlife Service Biological Opinions under the Endangered Species Act For two decades or more, the Corps of Engineers and the Fish and Wildlife Service have consulted on Missouri River dam and reservoir op- erations under the Master Manual and with regard to species of interest, under the Endangered Species Act, as well as the Coordination Act. In April 2000, the Corps of Engineers asked the Fish and Wildlife Service to consult under the Endangered Species Act with regard to Master Manual revisions, including (1) operations of the Missouri River mainstem system, (2) related operations of the Kansas River tributary reservoirs, and (3) operation and maintenance of the Missouri River Bank Stabilization and Navigation Project. The Corps had identified four listed species in the project area: the endangered pallid sturgeon (Scaphirhynchus albus), the endangered least tern (Sterna antiallarum), the threatened piping plover (Charadrius melo- dus), and the threatened bald eagle (Haliaeetus leucocephalus). The Corps Biological Assessment in early 2000 concluded that its op- erations of the Missouri River Mainstem System, and related operations of the Kansas River Tributary Reservoirs, and operations and maintenance of the Missouri River Bank Stabilization and Navigation Project were detri- mental to the survival and recovery of the endangered pallid sturgeon and interior least tern, the threatened northern Great Plains population of the piping plover, and the bald eagle. The Fish and Wildlife Service and the Corps then entered into a formal consultation process in April 2000 to address effects of the Corps operations of the Missouri River on the listed species. The Fish and Wildlife Service determined through the consultation process that Corps Missouri River operations posed jeopardy to the con- tinued existence of the listed species. The two agencies then collaborated to develop a Biological Opinion, and in 2000 the Fish and Wildlife Service issued a Biological Opinion that contained a description of current river operations, current status of the species, an environmental baseline, and a conclusion that the referenced Corps actions were likely to jeopardize the continued existence of the least tern, piping plover, and pallid sturgeon, but would not jeopardize the bald eagle. The Fish and Wildlife Service further concluded that to avoid jeopardizing the continued existence of the tern, plover, and sturgeon, it was necessary to (1) restore a portion of suitable riverine aquatic habitats and hydrologic conditions necessary for successful reproduction and recruitment of the three listed species, and (2) provide population augmentation (in the near term) for the pallid sturgeon to ensure genetic viability of the species until the necessary habitat and hydrologic conditions are restored. The Fish and Wildlife Service, working with the Corps, defined an RPA

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58 MiSSOuRi RivER PlANNiNg deemed necessary to avoid jeopardizing the least tern, piping plover, and the pallid sturgeon. The following text summarizes those RPA elements relevant to this report’s sediment-related tasks. Flow enhancement below Fort Peck Dam, unbalanced system regulation, and pallid sturgeon propagation are described elsewhere (USFWS, 2000). Flow Enhancement Below gavins Point Dam. Implementation of a spring rise and summer drawdown from Gavins Point Dam (river mile 811) was required by the Service to achieve four outcomes: (1) provide a spawning cue to pallid sturgeon; (2) condition new and existing emergent sandbar habitat for tern and plover nesting and chick rearing and adjacent shallow, slow-water habitat needed by both birds and fishes; (3) enhance aquatic habitat through connection of the main channel to backwaters and side channels to increase nutrients, invertebrates, and forage fish for larval and juvenile pallid sturgeon and adult and young least terns; and (4) scour sediments from pallid sturgeon spawning areas to increase the likelihood of egg survival. Habitat Restoration/Creation/Acquisition. The Fish and Wildlife Ser- vice directed the Corps to restore a portion of the historical Missouri River habitat to benefit the listed birds and fishes. Broad habitat restoration targets of 20-30 acres of shallow water per mile were defined, although the goals varied by river segments for emergent sandbar habitat (ESH) and shallow water habitat (SWH). Adaptive Management/Monitoring. The Corps was directed to imple- ment an adaptive management process that allowed modification of man- agement actions to benefit listed species in response to new information and to changing environmental conditions. One component of this process was establishment of an Interagency Coordination Team (ACT) to coordi- nate and guide development and implementation of a robust monitoring program to better understand baseline conditions, analyze actions, and implement modification as necessary to improve results. Recognize the Role of Sediment in Species Recovery. Most importantly for this report, the Biological Opinion recognized that sediment input was necessary to restore instream habitats and turbid waters: Initially, the Corps should determine the sediment deficit from natural con- ditions and the functional quantities needed to restore instream sandbars, and implement a pilot project at one of the main stem dams. . . . The Corps also should restore turbidity to functional levels downstream of Fort Peck, Fort Randall, and Gavins Point Dams. Turbidity will increase with actions taken to restore sediment transport; however, additional measures may be needed if reintroduced sediments are clean of small particulate matter that needs to be resuspended (USFWS, 2000, p. 213 pt. IV.B.) The Fish and Wildlife Service issued a Supplemental Biological Opinion

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59 MiSSOuRi RivER gOvERNANCE in 2003 that considered habitat conditions and new information not con- sidered in the 2000 Biological Opinion (for details of the 2003 Biological Opinion see USFWS, 2003). The 2003 Biological Opinion governs the operation of the system today. Key changes from the 2000 Biological Opinion include accelerated construction of shallow water habitat (with a research, monitoring, and evaluation adaptive management component) and modified flow enhancement requirements. (Chapter 4 describes current approaches to habitat restoration and adaptive management.) The Master Manual and Flow Modification: Shared Decision Making Through the NEPA Process The Master Manual is the guide used by the Corps to operate the system of six dams of the Missouri River Mainstem Reservoir System. It describes the Mainstem Reservoir System, including its Water Control Plan, and establishes operational policy for the multiple project purposes of flood control, hydropower, water supply, water quality, irrigation, navigation, recreation, and fish and wildlife. The Corps first undertook revision of the original 1960 Master Manual in 1989 when the basin was experiencing its first major drought since the system became operational. Additionally, federal listing of the interior least tern, piping plover, and pallid sturgeon underscored the need to revisit the Master Manual. The Corps also be- came more aware of its responsibilities to tribes as independent sovereign nations. The Corps’ objectives for the Master Manual were to develop a Water Control Plan to meet the contemporary needs of the basin, fulfill responsibilities to tribes, and comply with environmental laws, including the ESA. The 2000 and 2003 Biological Opinion were released in the midst of Master Manual revisions. Several Water Control Plan features were changed in the Master Man- ual, and these changes became part of the preferred alternative identified in the required Environmental Impact Statement (EIS) issued in 2004. As one example, the preferred alternative included minimum flows for peri- ods when navigation was not supported to provide for downstream power plants, municipal and industrial intakes, water supply, and water quality. An adaptive management process was also identified. However, because it was coincident with the Master Manual revision process, the Biological Opinion influenced but did not dictate decisions on operational rules. For example, the Biological Opinion called for a bimodal spring pulse release from Gavins Point Dam. Although the environmental impact statement addressed several alternatives that included spring pulse releases, the pre- ferred alternative selected in the Corps Record of Decision (ROD) for the revised Master Manual did not include such releases. However, the ROD agreed that a spring pulse plan that would comply with provisions of the

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60 MiSSOuRi RivER PlANNiNg 2003 Amended Biological Opinion would be identified no later than 2006. Although the Record of Decision was challenged by various states and environmental groups, in the end, this plan was adopted (Jacobson and Galat, 2008). NEW STUDIES, NEW ORGANIZATIONS, CHANGING RESPONSIBILITIES The environmental impact statement and the updated Master Manual committed to the Corps to a new program in 2004, known as the Missouri River Recovery Program (MRRP), as well as creation of a stakeholder advisory group, the Missouri River Recovery Implementation Committee (MRRIC). The MRRIC was formally established through the federal Wa- ter Resources Development Act (WRDA) of 2007. To aid in the recovery effort, Congress also authorized the Missouri River Ecosystem Plan, or MRERP, under the 2007 WRDA (and described below in further detail). Subsequently, in 2009, Congress instructed the Corps to begin the Missouri River Authorized Purposes Study (MRAPS). Each of these authorities and studies bear some relation to decisions and planning being done under the Master Manual, the Biological Opinion, and the ongoing mitigation plan. Meanwhile, in 2007 the Missouri Clean Water Commission ordered the Corps to stop discharging sediments into the mainstem Missouri River during construction of mitigation projects along the river (the 2007 order was amended in March 2008). All these programs and institutions are described below. Missouri River Recovery Program In its 2004 Master Manual, the Corps committed to a different ap- proach to Missouri River decision making. The Master Manual ROD com- mits the Corps to river restoration actions that will be identified, reviewed, and implemented through a cooperative process that includes stakeholder representation and adaptive management. This Missouri River Recovery Program is a comprehensive effort, led by the Corps in partnership with the Fish and Wildlife Service, tribes, states, other federal agencies, and non- governmental organizations, to develop and implement actions to recover the Missouri River. The MRRP vision is for “a sustainable ecosystem supporting thriving populations of native species while providing for current social and eco- nomic values.” Its mission is to “implement actions to accomplish Missouri River ecosystem recovery goals in coordination and collaboration with agency partners and stakeholders.” Recovery efforts are coordinated by the Corps with funding that flows through the Corps budget (see http://

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61 MiSSOuRi RivER gOvERNANCE www.moriverrecovery.org/ mrrp/f?p=136:1:749223002111673::NO::: for details on the MRRP). The Corps of Engineers is expected to coordinate a variety of restora- tion activities while undertaking floodplain acquisition, habitat creation, river flow modifications, and research and assessment. The largest current recipients of Corps funding under the Biological Opinion are the Indepen- dent Science Program (ISP) and land acquisition under the ongoing Mitiga- tion Program. Missouri River Ecosystem Restoration Plan The Missouri River Ecosystem Restoration Plan was authorized under the 2007 Water Resources Development Act for the purpose of conducting a collaborative, long-term ecosystem restoration study. Under MRERP, the Secretary of the Army, in consultation with a stakeholder advisory group (MRRIC), will conduct a study of the Missouri River and its tributaries to determine actions required to (1) restore ecosystem functions, (2) mitigate habitat losses, and (3) recover native fish and wildlife on the Missouri River (see Box 3-1 for details on restoration, mitigation, and recovery concepts and definitions). The goal of the MRERP is to recommend priorities and objectives for Missouri River recovery, mitigation, and restoration while seeking balance with social, economic, and cultural values for future generations. Key socioeconomic values proposed for consideration include navigation, water supply, flood attenuation, power generation, recreation, and cultural resources. MRERP objectives include (1) considering ongoing programs related to mitigation, recovery and restoration; (2) identifying priorities for mitigation, recovery and restoration throughout the basin; (3) outlining a long-term adaptive manage- ment approach for restoration of the river; and (4) guiding future program and site-specific action development to ensure that overall restoration goals are met in the long term. An environmental impact statement is being developed for a comprehensive watershed plan that identifies priorities for ecosystem restora- tion in the Missouri River basin to be implemented by the Corps, the FWS, and others. The preferred alternative from this environmental impact statement will guide future recovery efforts throughout the Missouri River basin. The pres- ent deadline for completion of the MRERP study and publication of the final MRERP-EIS and Record of Decision is 2016. The scope of MRERP is broader and more integrative than that of past programs. It includes the mainstem Missouri River and its alluvial valley (floodplain) from Three Forks, Montana, to its confluence with the Missis- sippi River near St. Louis. Additionally, tributaries, bluff lands, and uplands may be added as necessary to consider targeted resources.

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62 MiSSOuRi RivER PlANNiNg BOX 3-1 Definitions of Mitigation, Recovery, and Restoration Currently Used Within the MRERP Mitigation consists of measures to avoid, minimize, or compensate for adverse impacts to the environment. The U.S. Army Corps of Engineers follows mitiga- tion provisions including the Water Resources Development Act of 1986, Water Resources Development Act of 2000, Water Resources Development Act of 2007, and Council on Environmental Quality regulations for implementing the National Environmental Policy Act. The Council on Environmental Quality regulations (40 CFR 1508.20) provide the basis of mitigation as a means to avoid or minimize environmental harm. This includes measures to rectify, reduce, eliminate, or compensate for the impacts caused by the action. Recovery is defined under the Endangered Species Act as “improvement in the status of listed species to the point at which listing is no longer appropriate” under the criteria set out in Section 4(a)(1) of the Act” (50 CFR 402.02). Restoration consists of separable features undertaken to return a degraded con- dition to a less degraded condition (ER 1105-2-100, Appendix C, Corps Planning Guidance Notebook [USACE, 2000]). The Corps of Engineers’ civil works eco- system restoration policy (EP 1165-2-502 [USACE, 1999] states that “the purpose of Civil Works ecosystem restoration activities is to restore significant ecosystem function, structure, and dynamic processes that have been degraded. Ecosys- tem restoration efforts will involve a comprehensive examination of the problems contributing to the system degradation, and the development of alternative means for their solution. The intent of restoration is to partially or fully reestablish the attributes of a naturalistic, functioning, and self-regulating system.” The intent of ecosystem restoration is to reverse the adverse impacts of human activity and restore ecological resources, including fish and wildlife habitats, to previous levels of productivity but not a higher level than would have existed under natural condi- tions in the absence of human activity or disturbance (ER 1105-2-100, Appendix C [USACE, 2000]). SOURCES: Wayne Nelson-Stastny, USFWS MRNRC Coordinator; Randy Sellers, USACE, Kansas City District, MRERP coordinator. Missouri River Recovery Implementation Committee In the Water Resources Development Act of 2007, the Secretary of the Army was directed to establish a Missouri River Recovery Implementation Committee (MRRIC) composed of federal, state, tribal, and nongovern- mental stakeholders. The MRRIC’s duties are to provide guidance on the Missouri River Ecosystem Restoration Program. Specifically, the MRRIC is to provide guidance to the Secretary of the Army on Missouri River recovery and mitigation plans. The MRRIC has roughly 70 members who

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63 MiSSOuRi RivER gOvERNANCE represent a wide array of local, state, tribal, and federal interests through- out the Missouri River basin. The committee has 28 seats that represent 16 nongovernmental stakeholder categories. In addition, eight states and 28 tribes have voting members. Thirteen federal agencies with programs affecting the Missouri River appoint non-voting representatives to MRRIC. The purpose and scope of the MRRIC is threefold. First, the MRRIC makes recommendations and provides guidance on the Missouri River Ecosystem Recovery Plan, which, as noted above, includes mitigating losses of aquatic and terrestrial habitat, recovering federally listed species, and restoring the Missouri River ecosystem to prevent further declines among other native species. Second, the MRRIC provides guidance on the Missouri River Recovery Program. This guidance includes changes to implementa- tion strategies as a result of lessons learned in the course of adaptive man- agement, as well as coordination of the development of consistent policies, strategies, plans, programs, projects, activities, and priorities. Lastly, the MRRIC’s recommendations must identify potential impacts to stakeholders and means of avoiding, minimizing, or mitigating adverse impacts. The MRRIC has made recommendations for an engagement strategy between it and the Corps on the MRERP. Most relevant to this report, the MRRIC recommended that the study include sediment and river morphol- ogy dynamics throughout the basin, including channel degradation, sedi- ment levels below reservoirs, and the relationship of sediment deposition on the functionality of reservoirs (Missouri River Recovery Implementation Committee, Recommendations on Purpose and Need, Adopted by Consen- sus on July 23, 2009). The MRRIC also concluded that the MRERP study provides an excep- tional opportunity for a coordinated, basin-wide approach between federal, tribal, state, and stakeholder interests. MRRIC advised the Corps to iden- tify a single, comprehensive and integrated plan to guide the implementa- tion of programs associated with mitigation, recovery, and restoration activities in the Missouri River basin. It further advised that the Secretary rely on the MRRIC as the principal forum for discussing and adopting final provisions of this coordinated, basin-wide plan. The role of the MRRIC in influencing Corps’ decisions is evolving, and it is too early in its history to assess how it will affect federal policy for the Missouri River. Missouri River Authorized Purposes Study As noted at the beginning of this chapter, legally authorized Missouri River uses include flood control, navigation, irrigation, hydropower, water supply, water quality, recreation, and fish and wildlife. For years there have been differences of opinion and conflicts over how to best use the water and related resources of the dam and reservoir system among its many users. In

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64 MiSSOuRi RivER PlANNiNg addition to more traditional purposes and uses of the system, the ongoing Biological Opinion and the Missouri River Ecosystem Restoration Plan focus attention on native species protection and recovery. There is a great deal of competition for the river’s resources and great interest in the many trade-offs among its various authorized purposes. (Chapter 7 provides fur- ther comments regarding trade-off choices and resource limits.) Against this background, in the Omnibus Appropriations Act of 2009, Congress authorized the Corps to conduct the Missouri River Authorized Purposes Study (MRAPS). The act directs the Secretary of the Army to review the original project purposes of the Flood Control Act of 1944 to determine if changes to the authorized project purposes and existing federal water resource infrastructure may be warranted. The study was begun in October 2009, with an authorized cost of $25 million, and is scheduled to be completed in five years (more information on the study is available at: http://www.mraps. org/). The study is independent of the Missouri River Recovery Program and MRRIC; however, given the substantial overlap among MRAPS, MRRP, and MRRIC, clarification of lines of authority may be necessary. THE CLEAN WATER ACT, STATE WATER QUALITY RULES, AND SEDIMENT In considering sediment management on the Missouri River, it is im- portant to understand not only provisions of the Endangered Species Act, but also provisions of the Clean Water Act (CWA), especially the setting of ambient water quality standards for sediment and phosphorus concentra- tions. In many settings and river systems across the country, as well as in some streams throughout the Missouri River basin, sediment is considered to be a pollutant. As such, discharge of sediment is subject to regulatory limits, and reducing sediment runoff is a focus of many agricultural man- agement practices. Under the Clean Water Act, states are responsible for setting water qual- ity standards that meet the broad goals of the act: restoring and maintaining the chemical, physical, and biological integrity of the nation’s waters. Water quality standards begin with state identification of designated uses for each state waterbody. Once designated uses are set, the state adopts measurable criteria that ensure that designated uses are met. These criteria may be nar- rative or numeric. Narrative criteria are descriptive of desired biological conditions for a river. Numeric criteria specify the acceptable frequency, duration, and magnitude of the presence of a pollutant (e.g., turbidity mea- sure, phosphorus concentrations) or a waterbody condition (benthic or fish community index). In addition, the criteria are expected to be protective of downstream waters. Although states are responsible for water quality criteria, the Environmental Protection Agency (EPA) is expected to exercise

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65 MiSSOuRi RivER gOvERNANCE oversight on criteria. In interstate waters, such as the Missouri River, EPA can lead efforts to harmonize uses and criteria among states. The Clean Water Act and Corps of Engineers Missouri River Mitigation Projects In an order issued in September, 2007, and later amended in March, 2008, the Missouri Clean Water Commission (CWC) ordered the Corps to stop discharging sediments into the Missouri River until the Corps could prove they were not impacting water quality in Missouri (also see Perry, 2007). The Corps interprets the Biological Opinion as requiring it to in- crease turbidity in the river and hence it is encouraged if not mandated, pursuant to the Endangered Species Act, to discharge sediments for habitat mitigation projects into the river. Generally speaking, the commission ac- cepts that the Biological Opinion calls for habitat construction, but that it does not require discharge of sediments into the mainstem Missouri River. As discussed later in this report (Chapter 6), it is possible to develop water quality criteria that are consistent with the Clean Water Act and that do not conflict with Biological Opinion requirements for the Missouri River. For example, closer investigation of the legislative history and origins of the Clean Water Act show that it long has been recognized that historic watershed conditions can be a template for setting water quality uses and criteria. The Senate Report that accompanied the original Clean Water Act legislation refers to the “natural . . . integrity” of the nation’s waters, and highlights “the importance of historical records on species composition, ecological studies, and estimations of what a ‘balanced natural ecosystem’ should look like” [S. Rep. No. 92-414, reprinted in 1972 U.S.C.C.A.N. at 3716. Similarly, the 1972 House Report describes “integrity” as “a condi- tion in which the natural structure and function of ecosystems is main- tained” H.R. Rep. No. 92-911, at 76 (1972), reprinted in Congressional Research Service, A Legislative History of the Water Pollution Control Act Amendments of 1972, at 763 (1973)]. Current understanding of the historic sediment and related nutrient conditions in river segments and in the tributaries, as described in Chap- ter 2, provides just such a template. That chapter lays a foundation for interpreting the rules governing discharges of sediment to the river. As was explained in Chapter 2, sediments differ in their characteristics, the sources of sediments differ, and the sediment and nutrient history of each segment and each tributary is different. It therefore would be expected that not only would water quality criteria differ across segments and tributaries, but that rules governing sediment discharges would differ as well. In “clear water seg- ments,” sediment discharges would be limited by regulations that apply to all sources. In segments where the historic reference condition suggests sediment

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66 MiSSOuRi RivER PlANNiNg loads of certain grain and nutrient composition, then discharges consistent with those criteria would be allowable. However, if the segment-specific and tributary-specific criteria are to be met, then under the Clean Water Act, rules governing sediment discharges appropriate to that receiving water will apply uniformly to all sources of sediment, including sources from private lands, public facilities, and Corps of Engineers restoration activities. SUMMARY Congress continues to create authorities and responsibilities that leave the Corps effectively as the “water master” of the Missouri River, and hence sediment manager, as well. Congress authorized the Corps to execute MRERP and the authorized purposes study, and to propose plans to update and synchronize the multiple legislative directives under which the Corps now operates. Meanwhile, Congress created MRRIC to strengthen shared decision making, but MRRIC has only recently begun its operation and its roles and responsibilities have yet to be clarified. The role of MRRIC in relation to the role of the Corps will need to be defined within the setting of occasional cross-purposes of river users, limits of the river’s resources to meet all user demands, and the increasing powers and responsibilities of multiple federal, state, and tribal agencies granted by environmental laws, especially the Endangered Species Act. In the decades immediately following authorization of the Pick-Sloan Plan, the Corps of Engineers played a clear role as the water master of the Missouri River and its dam and reservoir system. Today, however, the setting of Missouri River governance is very different. For example, several recent, major river management initiatives and studies—such as the 2000/03 Biological Opinion and the mitigation program—have added greatly to compliance requirements for the Corps. In addition, states, tribes, commercial interests, and nongovernmental or- ganizations now seek a more active voice and role in river management decisions. At the same time, the Corps of Engineers retains authority to operate the Missouri River dam and reservoir system. These many changes have complicated the Missouri River governance structure for the Corps and others as they try to reach agreement on programs such as Biological Opinion program implementation, broader ecosystem recovery, and sedi- ment management planning. The Missouri River Recovery and Implementation Committee has the potential to play a central role in building consensus among a broad group of federal agencies and stakeholders in matters related to water and sedi- ment management. To help realize that potential, the Assistant Secretary of the Army for Civil Works should periodically review the MRRIC mission statement, operational rules, and accomplishments; implement modifica- tions to the mission, rules, and operations as deemed appropriate; and report its results to the Congress.