1
Introduction

Flowing a distance of roughly 2,300 miles through the heart of the continental United States, the Mississippi River is a resource of great economic value, environmental importance, and cultural and historical significance. The Mississippi River also is notable for the size of its drainage basin area: extending over much of the vast expanse between the Appalachian and the Rocky Mountains, it is the world’s third-largest river basin. With an area of more than 1.84 million square miles, it covers approximately 40 percent of the conterminous United States. The basin extends over all or part of 31 U.S. states and two Canadian provinces.

The Mississippi River has long been important for commercial transportation and navigation. Today, hundreds of millions of tons of commodities are shipped annually on the river, and the Greater Port of New Orleans and Baton Rouge handles more grain tonnage than any other port in the world (Port of New Orleans, 2006). The river and its floodplain ecosystem also provide numerous environmental goods and services, such as the Upper Mississippi River National Wildlife and Fish Refuge, the longest river refuge in the continental United States. The river’s extensive and multiple values prompted the U.S. Congress to pass the Upper Mississippi River Management Act of 1986, which designates the upper river “as a nationally significant ecosystem and a nationally significant commercial navigation system” (P.L. 99-662). The Mississippi River also is used as a source of drinking water for millions of people in cities along the river. Ensuring adequate water quality in the Mississippi River clearly is a national concern. Despite the importance of the river and its water quality, however, more effective Mississippi River water quality monitoring and



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1 Introduction F lowing a distance of roughly 2,300 miles through the heart of the continental United States, the Mississippi River is a resource of great economic value, environmental importance, and cultural and his- torical significance. The Mississippi River also is notable for the size of its drainage basin area: extending over much of the vast expanse between the Appalachian and the Rocky Mountains, it is the world’s third-largest river basin. With an area of more than 1.84 million square miles, it covers approximately 40 percent of the conterminous United States. The basin extends over all or part of 31 U.S. states and two Canadian provinces. The Mississippi River has long been important for commercial trans- portation and navigation. Today, hundreds of millions of tons of com- modities are shipped annually on the river, and the Greater Port of New Orleans and Baton Rouge handles more grain tonnage than any other port in the world (Port of New Orleans, 2006). The river and its floodplain ecosystem also provide numerous environmental goods and services, such as the Upper Mississippi River National Wildlife and Fish Refuge, the lon- gest river refuge in the continental United States. The river’s extensive and multiple values prompted the U.S. Congress to pass the Upper Mississippi River Management Act of 1986, which designates the upper river “as a nationally significant ecosystem and a nationally significant commercial navigation system” (P.L. 99-662). The Mississippi River also is used as a source of drinking water for millions of people in cities along the river. Ensuring adequate water quality in the Mississippi River clearly is a na- tional concern. Despite the importance of the river and its water quality, however, more effective Mississippi River water quality monitoring and 

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT management are confounded by administrative, historical, environmental, and other factors. Water quality programs for the Mississippi River are administered in accordance with the federal Clean Water Act (CWA). At the federal level, Clean Water Act implementation is the responsibility of the U.S. Environ- mental Protection Agency (EPA). States that border the river also have significant CWA-related management responsibilities, for many of which they have been delegated authority by the EPA. The fact that the Missis- sippi River flows through or borders on 10 different states (Figure 1-1) is 95° 90° MINNESOTA 90° Mississip R. pi 45° 45° WISCONSIN Minneapolis La Crosse R. sin Wiscon Dubuque IOWA River Quad Cities is no Illi 40° 40° ILLINOIS Missouri River 95° River io Oh St. Louis MISSOURI KENTUCKY r Rive TENNESSEE Arka ippi nsa Memphis sR ssiss 35° 35° i 85° Mi I ve PP r ARKANSAS SI SIS MIS L OU Vicksburg ISI Baton Rouge AN A 30° 30° New Orleans Atchafalaya R. 90° GULF OF MEXICO 0 150 300 mi 0 150 300 km FIGURE 1-1 Mainstem Mississippi River. © International Mapping Associates.

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 INTRODUCTION of no small consequence in implementing provisions of the Clean Water Act. These 10 states have different economies and land uses, different geo- graphical locations along the river, different social and economic priorities, and different levels of fiscal resources, all of which affect their Mississippi River water quality monitoring programs. In addition, the physical, chemi- cal, and biological characteristics of the river vary tremendously along its length, leading to different water quality issues and monitoring challenges in each state. Water quality issues in and along the river’s mainstem are fur- ther affected by land and water systems and practices in other states in the Mississippi River basin, for example, in upstream areas of large tributaries such as the Arkansas, Missouri, and Ohio Rivers. Mississippi River water quality monitoring and remediation efforts are also affected by historical and ongoing environmental changes along the river and through its river basin. Many of these changes have affected large areas and date back many decades or longer. On the upper river, con- struction of the series of navigation dams and pools in the 1930s as part of the 9-foot upper Mississippi River channel project initiated regional- scale hydroecological changes that continue today. Farther downstream, much of the lower river is separated from its natural floodplain by levees and other protective structures, some of which have been in place for 100 years. Losses of natural wetlands, which have been significant in all 10 states along the Mississippi River, date to nineteenth century efforts to drain these areas for agricultural and other human uses and are widespread. In addition to these historical changes to river hydrology and floodplain land uses, toxic substances (e.g., polychlorinated biphenyls [PCBs], dichlorodi- phenyltrichloroethane [DDT]), some of which persist in river sediments to this day, were discharged into the river prior to implementation of the Clean Water Act. There are also some continuing inputs of PCBs, DDT, and other toxic substances from stormwater sewers, runoff from urban streets and agricultural lands, and other sources due to the presence of residual contamination. Because there have been no periodic, large-scale assessments of the long-term status of legacy contaminants buried in the river’s sediments and carried in the tissues of the river’s biota, assessing the impacts of these legacy factors on the attainment of designated uses along the river has proven difficult. Many of these significant environmental changes to the river predate passage of the Clean Water Act, which was enacted in its present form in 1972. Remedial efforts aimed at improving water quality are often affected by these long-standing changes and thus are not readily addressed within the Clean Water Act framework. Many different federal, state, and nongovernmental groups have noted and studied these water quality issues and the challenges they pose to implementing the federal Clean Water Act and protecting Mississippi River

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT water quality. Questions about the effectiveness of the Clean Water Act and its implementation along the 10-state Mississippi River corridor prompted the McKnight Foundation of Minneapolis to request the National Research Council (NRC) to conduct a study of CWA implementation along the Mis- sissippi River. The McKnight Foundation and its Environment Program have long-standing interests in Mississippi River water quality. McKnight has also focused on building coalitions among varied groups along the river to help protect and restore water quality. With support from McKnight, the NRC’s Water Science and Technology Board (WSTB) convened the Committee on the Mississippi River and the Clean Water Act to conduct BOX 1-1 Committee on the Mississippi River and the Clean Water Act Statement of Task The study will review the experience of Clean Water Act implementation along the 10-state Mississippi River corridor. Part of the evaluation will include the review of the following reports: several GAO (formerly the General Accounting Office; now the Government Accountability Office) documents published in the late 1990s and early 2000s on Clean Water Act implementation, a January 2004 report from the Upper Mississippi River Basin Association on Mississippi River water quality, a November 2004 report from the Headwaters Group regarding Clean Water Act implementation on the Mississippi River, and a February 2003 petition to the U.S. EPA from the Sierra Club and EPA’s June 2004 response. These documents focus on issues of data collection, water quality, and programmatic and management challenges in implementing Clean Water Act regulations along the Mississippi River and will serve as a point of departure for the committee’s deliberations. Many concerns regarding Clean Water Act implementation and enforcement along the Mississippi River relate to the adequacy of water quality data, chal- lenges involved in establishing system-wide indicators and quality standards, compliance with standards and regulations, and interstate and interagency coor- dination and cooperation. The committee’s statement of task will accordingly be divided into four broad areas: Mississippi River Corridor Water Quality Problems, Data Needs and System Monitoring, Water Quality Indicators and Standards, and Policies and Implementation. 1. Mississippi River Corridor Water Quality Problems: Identify generally the key water quality problems through the 10-state Mississippi River system. The depiction of these problems should not only reflect varying conditions along the river corridor, but also discuss implications of Mississippi River water quality for conditions in the Gulf of Mexico.

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 INTRODUCTION a comprehensive study of the act’s administration along the river (Box 1-1 contains the committee’s statement of task). MISSISSIPPI RIVER WATER QUALITY ISSUES Mississippi River hydrology and ecology have changed fundamentally over the past 200 years. These changes have been driven by numerous ac- tivities including the construction of locks, dams, and levees, drainage of wetlands, agriculture, urbanization, and timber harvesting—all of which have affected Mississippi River water quality. In addition, many years of 2. Data Needs and System Monitoring: • Identify and discuss key water quality data needs for the 10-state Mississippi River corridor with regard to Clean Water Act reporting requirements. What are the main barriers to collecting and reporting these data? How could water quality data collection activities and programs for the Mississippi River corridor be revised to promote progress toward Clean Water Act objectives? • Identify and discuss the key challenges to monitoring changes to wetlands, backwaters, and other riverine features along the Mississippi River corridor. How could these monitoring challenges be best addressed and overcome? 3. Water Quality Indicators and Standards: • Identify and discuss the key challenges associated with establishing water quality indicators and standards in the 10 different states along the Mississippi River corridor. How could these processes be enhanced to ensure protection of downstream water quality? What benefits (if any) could be realized by making these procedures more uniform across the states? • To what extent does the Clean Water Act affect water quality in the Gulf of Mexico? Do means exist to develop water quality standards—in particular nutrient standards—in all 10 Mississippi River states that can ensure protection of water quality in downstream waters in the Gulf of Mexico? 4. Policies and Implementation: Identify and discuss the key challenges in administering Clean Water Act authorities and programs aimed at • National Pollution Discharge Elimination System (NPDES) permits, • Impaired waters designations, and • Protecting and restoring wetlands, backwaters, and other riverine features along the 10-state Mississippi River corridor. How could collaborative efforts within federal agencies, between federal agen- cies, and between the 10 Mississippi River states, be strengthened to enhance implementation of these Clean Water Act provisions?

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT variably controlled municipal combined sewer and stormwater discharges, and steadily increasing industrial activities along the river, have contributed to water quality degradation. Concerns regarding deteriorating water qual- ity in the nation’s waterbodies were reflected in passage of both the Federal Water Pollution Control Act Amendments in 1972 and the further 1977 amendments that gave the act its shorter name, the Clean Water Act (also subsequently amended in 1981, 1987, and 1990). Since the Clean Water Act’s passage, good progress has been made in many aspects of controlling “end-of-pipe” pollution from industries, municipalities, and other point sources to the Mississippi River. The focus of water quality improvement efforts generally has been on controlling these point sources through the act’s National Pollutant Discharge Elimination System (NPDES), a permit program for pollutant discharges. Point source pollution remains a problem in some stretches of the Mis- sissippi River and in the river basin. There are also water quality problems related to “legacy” pollutants in the river, along with emerging water qual- ity problems. The more pervasive Mississippi River water quality manage- ment challenge today is management of nonpoint sources of pollutants, especially nonpoint inputs of nutrients and sediments. These nutrients and sediments derive from a variety of activities, including agriculture, forestry, and increased urbanization. Mississippi River water quality also is affected by many large-scale hydrologic modifications along its mainstem, includ- ing the construction of locks, dams, and navigation pools, as well as levees along the lower river. A prominent example of the challenges posed by nonpoint source pollutants is the occurrence and persistence of a hypoxic (oxygen-deficient) “dead zone” in the northern Gulf of Mexico as a result of nutrient (nitrogen, in particular, but also phosphorus) inputs from the Mississippi River. Reductions of nitrogen and phosphorus in nonpoint source inputs to the Mississippi River are necessary to address this problem. Clearly there are important Mississippi River water quality issues beyond sediments and nutrients, such as point and nonpoint inputs of pathogenic microorganisms, toxic metals, and organic compounds, as well as the ef- fects of legacy pollutants. Sediments and nutrients, however, are the factors of primary concern because of the magnitude of their mass loadings into the river, their changes over time, and the scale of the associated ecological impacts. Under the Clean Water Act, the EPA and the states have joint respon- sibility for protecting, maintaining, and restoring water quality. In general, states designate specific uses for their waters; establish water quality criteria and, where required, maximum permissible discharge loadings to protect those uses; control pollutant sources through regulatory and nonregulatory measures; and monitor and assess water quality on an ongoing basis. States must submit periodic water quality assessment reports to the EPA, including

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 INTRODUCTION lists of impaired waters, and then take appropriate actions to protect and restore impaired waters through the development of TMDLs (Total Maxi- mum Daily Loads, which are discussed further in this report). The EPA has largely an oversight and coordination role in this process, establishing recommended water quality criteria and related elements of Clean Water Act administration (UMRBA, 2006). However, the EPA has authority to take action and lead when the objectives of the Clean Water Act are not being met by the states. The 10 states along the Mississippi River corridor differ in the extent to which they have focused on water quality in the Mississippi River com- pared to other waters within their respective boundaries. Smaller streams and rivers contained entirely within state borders do not create interstate jurisdictional issues under the Clean Water Act. Responsibility for water quality monitoring and management in the Mississippi and other large, interstate rivers, however, is not well defined by the Clean Water Act or other legislation. Federal and state agencies conduct some water quality monitoring on the Mississippi River, but there is no comprehensive and systematic program or initiative designed to oversee Mississippi River water quality monitoring, protection, or restoration. Thus, despite the value and importance of the Mississippi River, there is no clearly defined, river-wide framework for adequately monitoring and ensuring protection of its water quality—a theme that runs through this report. As specified in the charge to the committee, this report’s objectives are to identify key water quality problems along the 10-state Mississippi River corridor, review the experience of Clean Water Act implementation along the corridor in addressing these problems, and assess whether and how the Clean Water Act framework can be used to address the problems more ef- fectively in the future. Concerns regarding the management of nutrients and sediment loadings to the Mississippi River are key topics within this report, but a broad range of contaminants is also considered. Other issues relevant to Mississippi River water quality management that may be important to readers of this report, but were beyond the scope of this study, include in-depth analysis of remediation of legacy contami- nants across the river basin; valuation of environmental goods and services of the Mississippi River-floodplain ecosystems; possible amendments to the Clean Water Act; possible reallocations of federal and state resources de- voted to water quality monitoring; operational changes of upper Mississippi River dams and navigation pools; environmental justice considerations that may relate to localized water quality conditions along the river; cre- ation of new organizations for watershed and water quality management; efficiency of the existing TMDL process; and further analysis of cultural and historical differences among the 10 states along the Mississippi River corridor. While the importance of these and other issues is acknowledged,

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0 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT the committee focused its efforts and this report on the core Clean Water Act issues along the 10-state Mississippi River corridor as directed by its statement of task. This report is focused on the Clean Water Act and its implementation. The committee was not specifically charged to consider possible statutory changes to the Clean Water Act. The committee discussed this topic and chose to conduct its investigations and present its findings and recommen- dations entirely within the framework of the existing act. Although the committee focused its report on CWA implementation, the findings and recommendations herein provide a foundation that could be used for water quality management and restoration activities in realms beyond the act. REPORT ORGANIZATION AND AUDIENCE Following this introductory chapter, Chapter 2 reviews the charac- teristics of the Mississippi River basin, with an emphasis on features and activities that affect water quality in the river and into the northern Gulf of Mexico. Chapter 3 presents an overview of the key provisions of the Clean Water Act and can serve as a primer on this topic. Chapter 4 exam- ines key issues, advances, and challenges regarding implementation of the Clean Water Act along the 10-state Mississippi River corridor. Chapter 5 addresses logistical and administrative challenges in establishing and main- taining a water quality monitoring program on a large, interstate river such as the Mississippi. Chapter 6 discusses agricultural practices across the river basin and their implications for Mississippi River water quality. Chapter 7 explores institutional and policy modifications that could lead to more ef- fective implementation of the Clean Water Act for the Mississippi River and other large rivers of the nation. The report’s conclusions and recommenda- tions are printed in boldface in the Summary, as well as in each summary section at the end of the individual chapters. This report’s target audience includes federal and state elected officials, federal and state resource managers and scientists, experts in river and wa- ter quality science and policy issues, nongovernmental organizations with interests in Mississippi River and northern Gulf of Mexico water quality, and individual citizens along the river, across the basin, and along the Gulf Coast. Environmental protection and agricultural agencies for states in the Mississippi River basin comprise a special audience for the report because the states have primary responsibility for implementation of the Clean Water Act and coordination with other states. The U.S. EPA and the U.S. Department of Agriculture, as well as the U.S. Geological Survey, constitute another special audience for this report, because leadership and coordina- tion by these federal agencies will be crucial for more effective monitoring activities and for improving water quality in the Mississippi River and the northern Gulf of Mexico.