Mississippi River Water Quality and the Clean Water Act: Progress, Challenges, and Opportunities (2008)

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2 Characteristics of the Mississippi River System T he Mississippi River is one of the world’s and the nation’s great river systems. It ranks among the world’s 10 largest rivers in size, discharge of water, and sediment load, and its drainage area cov- ers 41 percent of the area of the conterminous 48 states (Milliman and Meade, 1983; Meade, 1995). With a length of roughly 2,300 miles, it is the second-longest river in the United States, exceeded in length only by the Missouri River (which is roughly 2,540 miles long and is the Mississippi’s largest tributary). The Mississippi River watershed extends from the Ap- palachian Mountains in the east to the Rocky Mountains in the west, and from southern Canada southward to the Gulf of Mexico (Figure 2-1). The Mississippi’s drainage area includes all or parts of 31 U.S. states; approxi- mately 70 million people live in the basin. The Mississippi River enters the Gulf of Mexico through two deltas: the Mississippi River proper through its larger delta southeast of New Orleans, Louisiana, and the Atchafalaya River delta, located to the west on the central Louisiana coast. The Mississippi River basin supports a high diversity and abundance of wildlife with their concomitant economic and social benefits. The Mis- sissippi River valley is as an important international migration corridor for waterfowl and the site of the Upper Mississippi River National Wildlife and Fish Refuge, which is the longest river refuge in the continental United States. The river and its tributaries support a rich fish and invertebrate fauna, including several threatened and endangered species, such as the pal- lid sturgeon and several mussels. The Mississippi River, particularly in its upper reaches, has important commercial and recreational fisheries; the Up- per Mississippi River National Wildlife and Fish Refuge hosts an estimated 21 

22 0.6 % 58% 18% 21% [w & w w 2.4 %] 500 km km land uses, and FIGURE 2-1  Mississippi River drainage basin, major tributaries,FIGURE 2-1 the Gulf of Mexico hypoxic area (as of 1999). SOURCE: Reprinted, with permission, from Goolsby (2000). © 2000 by the American Geophysical Union. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 23 119 fish species (USFWS, 2007). Although the full economic values of these ecosystem assets and services may not be measured readily through market transactions, the economic impacts of recreation on the upper Mississippi River economy have been estimated at well over $1 billion (in 1990 dollars) annually (USACE, 1994). In addition to these ecological resources, the Mississippi River serves as an important commercial transportation corridor. Hundreds of millions of tons of commodities are shipped annually on the Mississippi, and the river carries approximately 60 percent of the nation’s corn exports and 45 percent of its soybean exports (USACE, 2004). Navigation on the upper river is supported by 29 locks and dams that impound a series of navigation pools, which have had substantial impacts on river ecology and biota. The Mississippi River system’s biotic resources and value for recreation and water supply depend on suitable water quality, which is affected by nu- merous factors and inputs across its vast river basin. The Mississippi River receives contaminants from both point (i.e., a specific site, such as effluent from a sewage treatment plant or an industrial site) and nonpoint (i.e., unconfined and often unregulated sources, such as cropland) sources. The Mississippi River thus exhibits various kinds of water quality degradation and changes in different reaches. The river’s water quality is especially af- fected by nonpoint sources and, in particular, nutrient and sediment inputs (Meade, 1995; Howarth et al., 1996; Downing et al., 1999; Goolsby et al., 1999; NRC, 2000a; Figure 2-2). These nonpoint source pollutants derive from a variety of sources, including agricultural lands and city streets and yards. They also can be deposited on the landscape and surface waters from the atmosphere as a result of fossil fuel combustion and volatilization of ammonium from fertilizers and animal wastes. Applications of nitrogen and phosphorus fertilizers, primarily to row crops such as corn and soybeans, constitute the majority of nonpoint source pollutants (Howarth et al., 1996; Bennett et al., 2001; Turner and Rabalais, 2003; Figure 2-2). This chapter presents an overview of the characteristics of the Missis- sippi River and its large and varied watershed, with an emphasis on features and land use in the watershed that influence Mississippi River water quality. As this chapter explains, the quality of water in the Mississippi River basin reflects both natural processes and human influences across varying scales of time and space. The chapter is divided into four sections: Mississippi River physiography and population; historic alterations of the Mississippi River system and its river basin; Mississippi River water quality; and water quality impacts on the northern Gulf of Mexico. 

24 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Atmospheric Municipal and 4% industrial Waste 6% Fertilizers 56% Leguminous Crops 9% Manure 25% FIGURE 2-2  Relative proportions of point and nonpoint sources of nitrogen to the Mississippi River from the Mississippi River basin. FIGURE 2-2 SOURCE: Based on Antweiler et al. (1995) and Goolsby et al. (1999). THE MISSISSIPPI RIVER BASIN Physiography and Population Physiography The Mississippi River system stretches from the river’s headwaters at Lake Itasca in Minnesota southward through the heart of the continental United States, to the river’s mouth at the Gulf of Mexico. The mainstem of the Mississippi River passes through or borders 10 states—Minnesota, Wisconsin, Iowa, Illinois, Missouri, Kentucky, Tennessee, Arkansas, Missis- sippi, and Louisiana. The Mississippi River is fed by several large tributary streams, including the Ohio River, the Missouri River, the Arkansas River, and the Red River. The Missouri River subbasin constitutes 42 percent of the Mississippi River basin area and dominates the Mississippi basin’s land surface (Figure 2-3). Other major subbasins are the Ohio, Arkansas, and Red River subbasins, which comprise approximately 16, 13, and 7 percent of the entire river basin, respectively. The upper and lower Mississippi River basins comprise about 15 and 7 percent, respectively, of the surface land area that can affect Mississippi River water quality. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 25 FIGURE 2-3  Major subbasins of the Mississippi River watershed. SOURCE: Goolsby et al. (1999). FIGURE 2-3 Landforms and landscape features affect runoff rates and the ability of the land to absorb water before it runs into waterways, both of which can affect water quality. Most of the Mississippi River basin is formed on low plateaus and the high plains (Hunt and Trimble, 1998). The eastern side of the basin borders the Appalachian Mountains, while the basin’s western portions extend to the Continental Divide in the Rocky Mountains. Low plateaus across much of the basin generally are less than 1,000 feet in eleva- tion, while the High Plains region in the Missouri and Arkansas watersheds ascends to the west and reaches elevations of 5,000 feet above sea level at the base of the Rockies. The area north of the Ohio and Missouri Rivers was glaciated during the Pleistocene Era, and these landscapes are mostly flat to gently rolling ground moraines. Pleistocene glaciers left large areas of the midwestern United States, especially areas in Wisconsin and Minnesota, as wetlands and lakes. Over the past 150 years, many of the basin’s wetlands and swamps—which have significant capacity to slow runoff and floodwaters 

26 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT and to trap and filter potential pollutants before they reach the Mississippi River—have been drained for agriculture (and, to a lesser extent, for urban development) and now are largely productive croplands (Prince, 1997). Natural wetlands and gentle slopes, however, do not characterize all of this area. For example, the “Driftless Area” between Red Wing, Minnesota, and Dubuque, Iowa, was not affected by at least the most recent stage of gla- ciations. Unlike the more subtle terrain of surrounding areas, the Driftless Area has picturesque bluffs, steep slopes, and local relief of several hundred feet. The region of the basin lying to the south of the Ohio and Missouri Rivers consists largely of unglaciated low plateaus, except for the broad Mississippi River valley below Cairo, Illinois. In many places—for example, along the river at Vicksburg, Mississippi—old coastal plain material is cov- ered with alluvial deposits of the Mississippi River and its tributaries and with windblown loess from the upper Midwest deposited after the last ice sheets retreated some 10,000 years ago. Approximately 60 percent of the river basin consists of agricultural land (Figure 2-1), and the central portion of the basin, extending from Iowa to Ohio and from the Ohio and Missouri Rivers northward almost to the Canadian border, supports extensive croplands. The area is generally flat to rolling with hot, wet summers having long days (i.e., >15 hours of daylight in many areas for much of the summer). This region is known as the “Corn Belt,” but today it produces large amounts of both corn and soybeans. In the basin’s more arid areas to the west, more drought-tolerant crops (e.g., wheat) are grown (see Fremling, 2005, for more detail on Mississippi River geology and landforms). Population Population distribution affects the different types and amounts of pol- lutants that reach the Mississippi River. For example, industrial point sources tend to be concentrated in cities, agricultural nonpoint sources tend to be in rural areas, and industrial sources tend to contribute more toxic pollutants than do rural areas. Population centers also are more likely to be the points of wastewater discharges. Given its large area, different parts of the Mississippi River basin have different—and sometimes widely dis- parate—population densities. Population density in the Mississippi River basin is approximately 6 people per square kilometer, which is relatively low in comparison to similar figures from, for example, the Chesapeake Bay watershed (90 people per square kilometer) or Long Island Sound (200 people per square kilometer). Most (58 percent) of the basin’s 71 million inhabitants live in cities or metropolitan areas with a population of 500,000 or more (U.S. Census Bureau, 2007). During 1990-2000, population in every Mississippi River 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 27 basin state grew, and the region defined by the U.S. Census Bureau as the “Midwest” grew at a rate of 7.9 percent (U.S. Census Bureau, 2007). Not all sections of the basin are experiencing population growth, however, and many rural counties in the basin are experiencing population declines. For example, most of the basin’s population growth in the Midwest tends to be concentrated in its larger urban areas, such as Sioux Falls, South Dakota, and Minneapolis-St. Paul, Minnesota, which are growing rapidly. Stresses on the Mississippi River system are affected by these differ- ences in landforms and in human population within the river’s subbasins, and by the capacity of receiving waters to dilute and otherwise reduce the effects of the specific types of pollutants generated in different locations. For example, some contaminants, such as fecal coliforms and some urban industrial toxic substances, are effectively diluted as they move down- stream. Similarly, some toxic contaminants degrade or are sorbed to sedi- ment and settle out. In contrast, other pollutants, such as some herbicides and pesticides, accumulate with distance downstream, either in the water itself or in the tissues of living organisms (Nowell et al., 1999). Precipitation and Hydrology The Mississippi River basin spans several climate zones, which affect the timing and amounts of rainfall (and pollutants) entering the river at various points along its path. The eastern and southern portions of the Mississippi River watershed generally receive more rainfall than the west- ern and northern portions. Annual average values range from 60 inches or more in the southern Appalachian Mountains and along the Gulf Coast to 10-15 inches in the basin’s westernmost portions. The northern half of the basin experiences a continental climate, with warm to hot summers and ex- tremely cold winters, while the southern coastal region experiences a humid subtropical climate. In the north-central part of the basin, where agricul- tural activity is most intense, annual precipitation averages about 30 to 40 inches, with a pronounced summer maximum. Annual rates of evaporation vary greatly across the basin, ranging from 2-2.5 feet in the northeastern portions of the basin to as much as 5 feet in the southwestern part of the basin. The resulting annual runoff (precipitation minus actual evaporation) ranges from more than 20 inches in the east to less than 0.5 inch for much of the western part of the basin. The central agricultural region yields about 8-15 inches of runoff per year (Gebert et al., 1987). Although the Missouri River watershed is roughly 2.5 times larger than the next largest of the Mississippi River’s six major tributary watersheds   Midwestern states listed in this category include Illinois, Indiana, Iowa, Kansas, Michigan, Minnesota, Missouri, Nebraska, North Dakota, Ohio, South Dakota, and Wisconsin. 

28 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT (Figure 2-3), average annual Ohio River discharge is three times larger than that of the Missouri River. The Ohio River discharges more water into the Mississippi River than any of the river’s major tributary streams (Figure 2-4 and Table 2-1). As illustrated in Table 2-1, the Ohio River watershed deliv- ers 38 percent of the Mississippi River’s flow, measured in terms of mean annual discharge. In comparison, the upper Mississippi River contributes 19 percent of the total of Mississippi River discharge into the Gulf of Mexico, followed by the Missouri River and the lower Mississippi River (13 percent each), the Arkansas River, and the Red River. Figure 2-4 illustrates the very different hydrologic character of the Mississippi River above and below Cairo, Illinois, which is located at the confluence of the Mississippi and the Ohio Rivers. The stark difference in upper and lower Mississippi River hydrology is important in the context of this study and is considered a crucial distinction throughout this report. In addition to differences in discharge values and physical character across the river basin, Mississippi River flow varies seasonally and from FIGURE 2-4  Relative freshwater discharge of Mississippi River tributaries to the amount delivered to the northern Gulf of Mexico. Widths of the river and its tribu- FIGURE 2-4 taries are exaggerated to indicate relative flow rates. SOURCE: Meade (1995). 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 29 TABLE 2-1  Relative Proportions of the Mississippi River Watershed Within Its Larger Subbasins Land Area Discharge Watershed (%) (%) Upper (includes 5 and 6 in Figure 2-3) 15 19 Missouri 42 13 Ohio 16 38 Arkansas 13 10 Lower Mississippi 7 13 Red 7 7 SOURCE: Reprinted, with permission, from Turner and Rabalais (2004). © 2004 by Springer Netherlands. year to year (Figure 2-5). In general, peak average flows—22,500 cubic meters per second—occur in March, April, and May, while low average flows—as little as 7,000 cubic meters per second—occur in late summer and early fall. The timing of water discharge affects the flux of materials from the basin’s various landscapes. The timing, distribution, and temporal change of discharge volume into the northern Gulf of Mexico also affect both the physical oceanography and the biological processes leading to seasonal hypoxia (oxygen depletion). (See the section on Mississippi River water quality and the Gulf of Mexico for further discussion of hypoxia.) HISTORIC ALTERATIONS OF THE MISSISSIPPI RIVER SYSTEM Over the past two centuries, land use changes across the Mississippi River watershed and hydrologic changes along the length of its river- floodplain ecosystem have had significant impacts on water quality in both the Mississippi River and the Gulf of Mexico. One important land use change across the watershed has been substantial applications of ni- trogen- and phosphorus-based fertilizers in the last half century, primarily to increase production of row crops. The region’s land cover has changed dramatically, with vast areas of forests and prairies having been trans- formed into agricultural and urban lands. The river basin has also seen the drainage and conversion of millions of acres of wetlands, with more than one-half of the original wetland ecosystems having been converted to other land uses (Prince, 1997). Along the length of the river, key changes include the completion of a large hydropower dam at Keokuk, Iowa, in 1913; sub- sequent construction of locks, dams, and navigation pools as part of the 1930 Upper Mississippi River Navigation Project; and construction of flood protection levees along the entire river, especially in its lower reaches. This 

30 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT FIGURE 2-5  The 92-year annual average water discharge time-series data for the lower Mississippi River, Atchafalaya River, and combined flow. The lower panel FIGURE 2-5 shows the flow ratio (Atchafalaya River to total flow) for the same period.. Points are centered, decadal running-mean-averaged values (last values are partially ex- trapolated). Dashed horizontal lines are 92-year average values. Lower Mississippi River gauging station is located at Tarbert Landing, La. Atchafalaya River gauging station is located at Simmesport, La. SOURCE: Reprinted, with permission, from Bratkovich et al. (1994). © 1994 by Estuarine Research Federation. section discusses these changes as reflected in (1) land uses and wetlands, (2) navigation improvements on the upper Mississippi River, and (3) levee construction along the lower Mississippi River. Land Uses and Wetlands The conversion of vast areas of Mississippi River basin prairies and forests to cropland and other agricultural land following European settle- ment has had tremendous implications for Mississippi River water qual- ity. Large areas of virgin forests across the basin had been cleared in the 1850s, and by 1920 they were reduced largely to remnant forests (Greeley, 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 31 1925). In the State of Ohio, for example, forest cover was reduced from 54 percent in 1853 to 18 percent in 1883 (Leue, 1886). The conversion of land to agriculture also inspires use of fertilizers and pesticides, which can become river pollutants. The main use of land today in the Mississippi River basin is agriculture (58 percent of land use). Other land uses are range and barren land (21 percent), land types are woodland (18 percent), wetlands and water (2.4 percent), and urban land (0.6 percent; see Figure 2-1). Nevertheless, some forests are being reestablished today in parts of the river basin. Reversion of large areas of cropland in the eastern part of the basin since the 1920s has allowed regrowth of forest in part of the north-central region of the basin, some of which was in the “Prairie Archipelago” (Kuechler, 1975). Suppression of fire, reduced grazing, and expansion of land conservation by states and private organizations also have contributed to forest regrowth in certain areas. Wetland ecosystems, once ubiquitous in the Mississippi River basin, serve important functions in regulating runoff and in reducing runoff of pollutants. Large losses of wetland areas, many of which were drained for conversion to agricultural land along the Mississippi River, have eliminated most of the natural buffering systems that could help reduce runoff of pol- lutants, toxic substances, and nutrients into the Mississippi River tributaries and mainstem (Table 2-2). Specifically, within the Mississippi River valley it is estimated that 56 percent of the wetlands have been lost to agriculture, navigation, reservoirs, and levees (Winger, 1986). Across the United States, similar rates of wetland losses have occurred. More than half of the original TABLE 2-2  Wetland Losses in the Mississippi River Mainstem States State Percent Loss (circa 1980s) Estimated Wetlands Remaining (acres) Minnesota 42 8,700,000 Wisconsin 46 5,331,392 Iowa 89 421,900 Illinois 85 1,254,500 Missouri 87 643,000 Kentucky 81 300,000 Tennessee 59 787,000 Arkansas 72 2,763,600 Mississippi 59 4,067,000 Louisiana 46 8,784,200 Total 67 33,052,592 SOURCE: Dahl (1990). 

32 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT wetlands in the United States have been lost to drainage practices (Zucker and Brown, 1998), many of which are related to agricultural production in areas that originally were swampy and too wet to farm. Navigation Improvements on the Upper Mississippi River On the upper Mississippi River, most changes to river hydrology and ecosystems have been driven by Congress and the efforts of the U.S. Army Corps of Engineers to improve river navigation. For example, the Rivers and Harbors Act of 1866 mandated a 4-foot navigation channel. In 1878, Congress authorized construction of a 4½-foot channel, which required the building of wing dams, closing of backwater channels, and building of five headwater dams to help control downstream flow (see also Anfinson, 2003). In 1906, Congress authorized a 6-foot channel that necessitated more and larger wing dams and additional closings of secondary channels crossing back swamp areas. Despite this repeated channel deepening, the depth of the river channel for interstate commerce and transportation along the upper Mississippi River was not always dependable. Calls for a more reliable lock-and-dam system began in the late nineteenth century and increased in the early twen- tieth century. These discussions included some bitter controversies between navigation interests, on the one hand, and railroads and emerging environ- mental interests, on the other (Anfinson, 2003). After many years of discus- sion, Congress authorized the Upper Mississippi River Navigation Project in 1930. The Corps of Engineers subsequently constructed a system of locks, dams, and navigation pools to support a 9-foot channel, and by 1940 there were 27 low-head dams between St. Paul, Minnesota, and St. Louis, Missouri (Figure 2-6). The upper Mississippi River (along with the Illinois River, where several dams have been constructed and which is considered by the Corps of Engineers as part of the same navigation system—the Upper Mississippi River-Illinois Waterway—UMR-IWW—has promoted shipping and commerce in the region, as Mississippi River freight traffic increased from 2.4 million tons in 1940 to 87 million tons in 2000 (Anfinson, 2003). Lock-and-dam system proponents maintain that the UMR-IWW is essential to the competitiveness of commercial shipping, while some project critics emphasize the large environmental changes and impacts caused by the dams and navigation pools. From the late 1980s until 2004, the Corps of Engi- neers conducted a feasibility study of the economic prospects of extending several locks along the lower portion of the UMR-IWW. The study was the most extensive in the agency’s history. It was completed in December 2004 when the final report recommended a $5.3 billion program for eco- system restoration and a $2.4 billion program for navigation infrastructure improvements. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 33 FIGURE 2-6  Locks and dams of the Upper Mississippi River-Illinois Waterway. SOURCE: NRC (2005). FIGURE 2-6 Levee Construction Along the Lower Mississippi River Large and extensive levees are the primary structures that affect flow and volume along the lower Mississippi River. There are no locks or dams across the Mississippi River below St. Louis. Levee construction in the 

34 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT lower Mississippi River began around 1717 and increased gradually until the 1880s, when the rate was accelerated (Barry, 1997). Following the di- sastrous 1927 flood in the lower Mississippi River region, the U.S. Army Corps of Engineers began an extensive flood control program of channel- ization and levee construction along the lower Mississippi, along with the establishment of floodways in Missouri and Louisiana. Levee construction has reduced considerably the natural floodplain of the Mississippi River basin and the natural aquatic ecosystems along its course (Table 2-3). Spe- cifically, levees have reduced the area of seasonally flooded wetlands along the river, and dikes and revetments used to entrain the channel prevent the river from creating new habitat. The reduced ability to form new habitats (which occurred historically as the river meandered) has had impacts on the floodplain, such as sedi- mentation of lakes on the lower Mississippi River in both oxbow lakes and other former channels (see Cooper and McHenry, 1989). In contrast to the upper Mississippi River, which has retained many of its larger backwater areas, fewer such backwater habitats remain along the lower Mississippi River. Levees have not been the only source of hydrologic changes in the lower Mississippi River. During the 1930s, for example, the Corps of Engineers and others dug channels across the necks of meander loops, thereby short- ening the river (Schumm and Winkley, 1994). The upper portion eventually filled with sediment, with the lower limb remaining as a link connecting the Mississippi, Atchafalaya, and Red Rivers. Eventually, the Atchafalaya River began enlarging itself through the capture of increasingly greater amounts of the Mississippi’s flow. To prevent the Atchafalaya River from becoming the main channel of the Mississippi River, a series of control structures was completed in 1962 (Reuss, 1998; McPhee, 1999). Today, a controlled amount of Mississippi River discharge—roughly 25 percent—is diverted to the Atchafalaya system, joining the Red River, to the Gulf of Mexico (Turner et al., 2007). TABLE 2-3  Losses of Floodplain Acreage Along the Mississippi River River Segment Floodplain Acreage × 1000 % of Floodplain Behind Levees Upper Mississippi (N) 496 3 Upper Mississippi (S) 1,006 53 Middle Mississippi 663 82 Lower Mississippi 25,000 93 Deltaic Plain 3,000 96 Totals 30,493 90 SOURCE: Delaney and Craig (1997). 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 35 Effects of Structural Modifications The hydrology of the vast Mississippi River basin system has been altered significantly by locks, dams, reservoirs and navigation pools, earth- work levees, channel straightening and bank stabilization, and spillways for purposes of flood protection, navigation, and water supply. These altera- tions have had numerous environmental impacts, including the transport and distribution of water, sediments, and dissolved materials (including nutrients and toxic substances), effects on the migration of fish and other aquatic species, submergence of aquatic vegetation, and the interruption of flow regimes. Large areas of the floodplain today are isolated by levees, the river is straightened and the flow is confined, large areas of floodplain in the upper river today are submerged under navigation pools, and many wetlands adjacent to the river have been drained. As a result, the spatial and temporal distributions of water velocities, bottom substrate, and water depths differ markedly from conditions that existed prior to the twentieth century. MISSISSIPPI RIVER WATER QUALITY Many Mississippi River water quality issues of today resemble the is- sues of the early 1970s, when the Clean Water Act was being drafted, but their relative importance has shifted in the past 35 years. Water pollution control measures (e.g., the National Pollutant Discharge Elimination Sys- tem, discussed further in Chapter 3) have reduced point source pollutant inputs from industrial and municipal discharges. This has, in turn, reduced many serious water quality problems such as oxygen depletion caused by organic wastes, thermal pollution, oil slicks, phosphate detergent wastes, and sediments from larger construction sites. In addition, removal of lead from gasoline and the banning of some industrial chemicals such as poly- chlorinated biphenyls (PCBs) and pesticides such as chlordane, aldrin, dieldrin, and DDT (dichlorodiphenyltrichlorethane) have greatly reduced the amount of toxic substances in the Mississippi River. Pretreatment pro- grams in larger cities have reduced discharges of heavy metals and other toxic materials from municipal wastewater treatment plants (see Chapter 4, Box 4-1 for further discussion of water quality improvements under Clean Water Act-related projects). Despite these advances, the Mississippi River today is affected by water quality problems and challenges that include nutrients, sediments, toxics, and fecal bacteria. Toxic substances—metals and organic chemicals—are primarily legacy contamination issues, although there are continuing in- puts, especially of pesticides. These substances have chronic ecosystem and human health impacts and are difficult to address, because river bottom 

36 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT sediments are the primary reservoir and source of these materials in many reaches of the river. High counts of fecal bacteria, once a public health problem at raw sewage discharges all along the Mississippi River, were substantially reduced with the implementation of secondary sewage treat- ment in many areas. Today, some parts of the river—mainly near large municipalities—still experience fecal bacteria counts that exceed water quality standards. Fecal bacteria and new inputs of toxic substances can be controlled through existing mechanisms in the Clean Water Act. By contrast, water quality problems related to nonpoint source inputs—especially (1) nutri- ents, primarily nitrogen and phosphorus from agricultural runoff and other agriculture activities, and (2) sediments, from upland or farmland erosion and river bed and bank erosion—are not as readily addressed by existing mechanisms. Accordingly, this report focuses primarily on Mississippi River water quality problems as they relate to nutrients and sediments. Nutrients Excess nutrient loadings cause marine algae to grow to great abundance and thereby affect coastal aquatic ecosystems, both in the Gulf of Mexico and around the world. The processes of algae decomposition ultimately lead to oxygen depletion and “dead zones” in coastal waters. The Gulf of Mexico is probably the best-known of these affected coastal ecosystems, but nutrient overenrichment affects coastal areas both elsewhere in the United States (e.g., Chesapeake Bay) and in sections of Asia, Europe, and South America. Moreover, according to a recent report from the United Na- tions Environmental Programme (UNEP, 2006), the number of these dead zones is increasing. These consequences stem from global human popula- tion growth and its associated activities that have, at accelerating rates, altered the landscape, hydrologic cycles, and flux of nutrients essential to plant growth, particularly in the last half-century (Vitousek et al., 1997; Galloway and Cowling, 2002; Galloway et al., 2003). To support the need for fuel, fiber, and food, humans have increased nitrogen and phosphorus loadings to aquatic and terrestrial ecosystems significantly, altering the global cycles of those nutrients. The excess nutrients affecting the Mississippi River-northern Gulf aquatic system derive primarily from diffuse, nonpoint sources (e.g., land runoff and atmospheric deposition) and stimulate a variety of ecological and related effects. This section discusses the role of nutrients in phyto- plankton growth, nutrient quantities and changes over time, sources of nutrients within the Mississippi River basin, and the effects of excess nu- trient loading. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 37 Phytoplankton Growth Plants of all types, including corn, soybeans, wheat, aquatic vegeta- tion, seaweed, and microscopic phytoplankton or algae, need nitrogen and phosphorus to grow. Crop plant growth will not continue or reach maximum productivity without adequate nutrients, and farmers generally use nitrogen- and phosphorus-containing fertilizers to supplement nutri- ents in the soil. Similarly, aquatic plants (including phytoplankton) will not grow without suitable dissolved nutrient supplies. A specific group of phytoplankton that is the base of many aquatic food webs, the diatoms, also requires silica, which is essential for the formation of their cell walls. As with crops, the addition of nutrients to ambient waters stimulates phy- toplankton growth. However, once nutrient loads cause aquatic systems to cross certain thresholds, the results are not entirely positive. Instead, excess nutrients can reduce water clarity and stimulate harmful algal blooms. They can also lead to oxygen depletion, which in some cases can cause reduced or lost fisheries production. Naturally low availability of nitrogen, phosphorus, or silica, either in absolute concentration or in relation to other nutrients, may limit phy- toplankton growth. As a result, introducing excess supply of the limiting nutrient will enhance phytoplankton growth. Phosphorus usually is consid- ered the limiting nutrient for phytoplankton growth in freshwater systems and nitrogen in marine systems (Rabalais, 2002), but other, perhaps mul- tiple, nutrients may be limiting. Thus, both the concentration of a nutrient and its abundance relative to other nutrients control the production and composition of phytoplankton. Excess phosphorus has caused notable water quality problems in freshwater systems, such as noxious and toxic algal blooms, decreased water clarity, and low dissolved oxygen conditions. Likewise, excess nitrogen and some- times phosphorus have led to algal blooms in estuarine and coastal marine systems with the same results. Nutrient Quantities The amount of nutrients in an aquatic system can be quantified by concentration, loading on and/or yield from a landscape in a watershed, and loading to waterbodies. Concentrations of silicate and various forms of nitrogen and phosphorus have been measured frequently since the 1950s at many locations in the Mississippi River and near the terminus of the Missis- sippi, both at St. Francisville and at New Orleans. Earlier data are available from the twentieth century, from 1905-1906 and from 1935-1936. Data from the lower Mississippi River show that the average annual nitrate con- centration rose from the 1960s through the early 1980s, and considerably 

38 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT more since the end of the twentieth century (Turner et al., 1998; Goolsby et al., 1999). Similar changes are seen throughout the Mississippi River basin (Figure 2-7). Nitrate load in the Mississippi River (the product of nitrate concen- tration × discharge) increased about 300 percent from the 1950s to the mid-1990s (Goolsby et al., 1999; Goolsby and Battaglin, 2001), whereas streamflow from the basin increased only 30 percent in the same period (Figure 2-8 and Bratkovich et al., 1994). Clearly, the most significant driver 5 AVERAGE NITRATE CONCENTRATION, IN mg/L as N 4.5 4 1905-1907 3.5 1980-1996 3 2.5 2 1.5 1 0.5 0 H N IA , IL IN MO IA A ,O ,M i, L s, ar, h, ois am ota ine r i, as ipp d lin ou Ce gh es b Mo iss r Il Wa iss kin nn s we iss De rM Mi s Mu Lo rM we we Lo Lo FIGURE 2-7  Comparison of average annual nitrate concentrations in 1905-1907 with those in 1980-1996 for the Mississippi River mainstem and some of its tributaries. SOURCE: Reprinted, with permission from Goolsby (2000). © 2000 by American Geophysical Union. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 39 2.0 30 streamflow MILLIONS OF METRIC TONS PER YEAR STREAMFLOW, IN THOUSANDS OF 25 CUBIC METERS PER SECOND 1.5 NITRATE – NITROGEN, IN 20 1.0 15 nitrate 0.5 10 0 5 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 FIGURE 2-8  Annual flux of nitrate from the Mississippi River basin to the Gulf of Mexico, 1955-1999, and mean annual streamflow, 1950-1999. SOURCE: Reprinted, with permission from Goolsby (2000). © 2000 by American FIGURE 2-8 Geophysical Union. of the change in Mississippi River nitrate load is the increase in nitrate con- centration, not freshwater discharge (Justic et al., 2002). Only 20 to 25 per- ´ cent of the increased nitrate load between the mid-1960s and the mid-1990s was attributable to greater runoff and river discharge, with the remainder due to increased nitrogen concentrations in the lower river (Donner et al., 2002; Justic et al., 2002). River discharge is governed by precipitation (less ´ evapotranspiration) that can be regulated only marginally by dams on the Mississippi River mainstem and its tributaries, because the mainstem upper Mississippi River dams do not create reservoirs, but navigation pools. Thus, nitrate loadings to the Mississippi River can be controlled effectively only through control of nitrate concentrations. The total nutrient discharge to the Gulf of Mexico from the Mississippi River is dominated by nitrogen, with a mass loading that is about an order of magnitude greater than the phosphorus loading. From 1980 to 2005, nitrogen loadings ranged from 0.8 million to 2.2 million metric tons per year. Over the same period, values of phosphorus loadings were between 0.08 million and 0.18 million metric tons per year (Aulenbach et al., 2007). 

40 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Thus, nitrogen is the primary nutrient of concern in the northern Gulf of Mexico and along much of the Mississippi River. Excess phosphorus is a concern in various Mississippi River backwaters and tributaries and has significant impacts in certain sections of the Mississippi mainstem. A good example is at Lake Pepin, on the mainstem Mississippi River in southern Minnesota. Algal blooms and other impacts from phosphorus loadings occur there, especially at low flows in the river, and a Total Maximum Daily Load (TMDL) for phosphorus is in development (MPCA, 2007). Phosphorus sometimes is important in the lower Mississippi, where it can be a limiting nutrient to phytoplankton growth in the spring, and in the immediate plume of the Mississippi River as it discharges to the northern Gulf of Mexico. Given the importance of both nitrogen and phosphorus in various forms, it is necessary to consider management of both of these nutrient inputs, which stem primarily from nonpoint sources. Nutrient Sources Nutrients reach waterways through several pathways—erosion of nutrient-bearing soils and sediments, natural dissolution from soils and sediments, runoff over land or through soils, atmospheric deposition, and point source discharges. Nitrogen can be converted from atmospheric gas to ammonia and nitrate by bacteria on the roots of leguminous plants. Nutrients in the Mississippi River basin originate from the same multiple sources, but mostly from diffuse nonpoint sources (Figure 2-9). Figure 2.9 shows mineralization of soil organic nitrogen as an estimated constant background input rate (based on an assumption of 3 percent nitrogen in soil organic material and mineralization at a constant annual rate of 2 percent). Figure 2-9 also shows that inputs of nitrogen from agricultural sources, especially fertilizer applications, have been increasing and now are equal in magnitude to the natural background input rate. About 90 percent of the nitrogen load reaching the Gulf of Mexico from the Mississippi River is from nonpoint sources, including approximately 58 percent from fertilizer and mineralized soil nitrogen. The remaining approximately 10 percent is from a mix of sources that includes primarily municipal and industrial point sources (Goolsby et al., 1999; see Figure 2-9). Most nutrients derived from the Mississippi River watershed are from its upper and middle portions (Goolsby et al., 1999). The dominant water- shed in terms of total nitrogen loading is the combined upper and middle Mississippi watershed (subbasins 5 and 6 in Figure 2-10), with contribu- tions of 35-45 percent, followed by inputs from the Ohio watershed at 28-30 percent. The total nitrogen and nitrate loadings from the Red and Arkansas River watersheds are relatively small compared to the others (less than 7 percent, each). Loadings of total phosphorus (Figure 2-10) and sili- 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 41 FIGURE 2-9  Annual nitrogen inputs from major sources in the Mississippi River basin, 1951-1996. Details of sources of data and methods for estimating inputs are in Goolsby et al. (1999). FIGURE 2-9 SOURCE: Goolsby et al. (1999). cate (not illustrated) are about equally divided among the combined upper and middle Mississippi, lower Mississippi, Ohio, and Missouri watersheds and are relatively high. The majority of the nitrogen and phosphorus flux— for example, 56 percent of the nitrate—is from above the confluence of the Ohio River with the Mississippi River, and it derives mainly from nonpoint agricultural sources (Goolsby et al., 1999; Turner and Rabalais, 2004). Atmospheric deposition contributes a small (approximately 10 percent) percentage of nitrogen loading to the Mississippi River (Figure 2-9). The highest levels of nitrate deposition—which results from the burning of fos- sil fuels—are in the upper to middle Ohio River basin (Figure 2-11). The deposition of ammonium is highest within the upper to middle Mississippi River basin and is attributed to the volatilization of ammonia from fertil- izers and animal wastes (Figure 2-11). Given the airborne nature of this pollutant, it may be more appropriately managed through the Clean Air 

42 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT FIGURE 2-10  Spatial distribution of the average nutrient yields in nine large basins during 1980-1996. FIGURE 2-10 SOURCE: Modified from Figure 4.5 in Goolsby et al. (1999). Act. This deposition, however, eventually contributes to the total loading of nitrogen that may have to be managed under provisions of the Clean Water Act. A coordinated effort to manage the nutrient content of the Mississippi River needs to account for the multiple sources of nutrients that affect wa- ter quality and the activities that generate them. Nutrient Uptake and Transformation The proximity of sources to large streams and rivers is an important determinant of nitrogen delivery to coastal waters receiving Mississippi River discharge. The uptake and removal of nitrogen in the smaller streams is greater than in the Mississippi River mainstem, where this rate may ap- 

FIGURE 2-11 + – FIGURE 2-11  Wet deposition of NH4 and NO3 averaged for 1990-1996 data from the National Atmospheric Deposition Program in each of the 133 accounting units that make up the Mississippi River basin. NOTE: Blue circles indicate where NADP and CASTNet (Clean Air Status and Trends Network) sites are co-located. 43 SOURCE: Goolsby et al. (1999). 

44 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT proach zero (Alexander et al., 2000). The entry location of nutrient loads to the Mississippi River system thus determines the relative influence of in- stream removal of nutrients through natural processes. Efforts to remove or reduce nutrients through management scenarios generally are more effective at the source of nutrient loads in smaller streams and rivers, rather than attempting to recover or mitigate nutrient loads once the nutrients enter the Mississippi River. This is not to say that river floodplain projects designed to help remove nutrients are not valuable. In fact, nutrient removal projects downstream may in some instances be easier to implement than in upstream reaches for a variety of reasons, including financial, administrative, and others. Some of these “nutrient farms” are being planned in floodplain areas along the Illinois River, for example, which is a large Mississippi River tributary that delivers significant amounts of nutrients into the Mississippi. The Metropolitan Water Reclamation District of Greater Chicago is providing financial support for these projects, which are located approximately 100 miles downstream of its sewage outfalls in Chicago. River water is diverted through a series of gated, shallow floodplain compartments and then re- turned to the river, with a goal of demonstrating that substantial nitrogen removal can be achieved at less cost than with proposed tertiary treatment sewage plants in Chicago (Hey et al., 2005a, 2005b). Existing and restored floodplains along the Mississippi and its major tributaries may reduce nitrogen loads to the Gulf during major flood events (25- to 500-year flood events) when floodplains are inundated. The “pulse” of nutrients delivered to the Gulf of Mexico during these events thus may be lessened. After the flood of 1993 in the upper Mississippi River basin, nitrogen and phosphorus in sediment deposits on the floodplains of the Mississippi and Illinois Rivers were well in excess of the growth require- ments of floodplain vegetation and represent nutrients that were trapped instead of delivered to the Gulf of Mexico (Sparks and Spink, 1998; Spink et al., 1998). In general, increased nitrogen loads to the Mississippi River are less likely to be taken up and transformed across the current Mississippi River basin than they were historically because of losses of the system’s natural assimilative capacity. The human-modified landscape and hydrology of the Mississippi River system over centuries, coupled with population growth, agriculture, industrialization, urbanization, increased combustion of fossil fuel, and increased use of fertilizers in the post-World War II era, all have reduced the capacity to remove contaminants naturally across the entire watershed. Today’s significant water quality problems in the Mississippi River basin and its offshore coastal waters are related to these landscape developments, coupled with increased nutrient loads derived primarily from agricultural fertilizers and activities. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 45 Effects of Excess Nutrients The loading of lakes, rivers, and coastal waters with previously scarce nutrients, such as nitrogen or phosphorus, usually boosts production of phytoplankton. In excess, these algae are linked to a number of problems in aquatic ecosystems, including murkier water, unpleasant odors and sights of decomposing algae, production of toxic substances, periods of oxygen depletion, and loss of important fisheries. High levels of phosphorus can degrade inland waters; turn pristine, clear lakes into weed-choked water- bodies; and accelerate bog succession. Excess levels of nitrogen seeping into groundwater can contaminate drinking water wells and supplies (see, for example, Burkholder et al., 1999; Gilbert et al., 2005). Elevated nitrate levels in drinking water have serious public health implications. They are especially dangerous for children under 6 months of age because nitrate robs their blood of oxygen and can cause “blue- baby” syndrome. Removing nitrate from drinking water supplies is also an expensive proposition, requiring the addition of denitrification treatment systems. Elevated nitrate levels have been a problem in some areas of the Mississippi River basin. For example, in the Ohio River watershed, water quality advisories are issued every spring in Columbus, Ohio, for excess nitrate levels in local waters (Mitsch et al., 2001). Excess nutrients in lakes, ponds, slow-moving streams, and brackish areas in the upper ends of estuaries often lead to blooms of cyanobacteria (blue-green algae) that produce toxic substances. Exposure of humans to these toxic substances through contact, inhalation of water spray, or oral ingestion can cause debilitating illness and even death. Recreational activities such as swimming and water skiing can result in exposure to con- taminated water, as can being on the water in recreational or commercial fishing. Little is known about the transfer of cyanobacterial toxins into the food web, but recent studies indicate that there may be both environmental effects and human health concerns (Rabalais, 2005). Sediments The functioning of natural backwater and floodplain ecosystems along the Mississippi River depends on delivery of sediment and nutrients during floods. At the same time, sediment regularly fills some channels and other deep areas of the system and must be removed to support recreation and navigation activities and to sustain wildlife habitat. A multitude of contami- nants (e.g., phosphorus, pesticides, heavy metals, PCBs) are often adsorbed onto or otherwise associated with sediment particles. Thus, many areas in the river system where sediment is deposited can become “hot spots” for a mix of plant nutrients and toxic substances. 

46 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Sediments from natural erosion, agricultural land loss, and bed and bank erosion that are suspended within the water column decrease water clarity, which often leads to water quality impairments. Soil erosion is also problematic because soil nutrients (especially phosphorus) and pesticides may be adsorbed onto soil particles and thus have the potential to pollute downslope or downstream. Furthermore, suspended sediments can become trapped behind dams and other engineered structures throughout the Mis- sissippi River basin. The results are (1) sedimentation and trapping of sediments in areas such as navigational pools and backwaters on the upper Mississippi River and within the Atchafalaya River basin and (2) sediment deprivation in the Mississippi River deltaic plain, where combined natural and human-caused factors are leading to loss of coastal wetlands and bar- rier islands. Sediment-related problems along the Mississippi River thus range from too much to not enough sediment in different sections along the length of the Mississippi River corridor and can result in impairments to ecosystems and water quality. Figure 2-12 illustrates relative sediment contributions from the Missis- sippi River and its main tributary streams (Meade, 1995). It is estimated FIGURE 2-12  Mississippi River suspended sediment discharge, around 1700 (es- timated) and 1980-1990. Values in millions of metric tons per year. Widths of the FIGURE 2-12 river and its tributaries are exaggerated to reflect relative sediment loads. SOURCE: Meade (1995). 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 47 that the load of suspended sediments to the Gulf of Mexico in 1700 was roughly double the average values from 1980 to 1999 and that the Missouri River clearly dominated that load (Meade, 1995). Under present conditions the Missouri River continues to dominate the load, but because of the construction of several large storage dam reservoirs on the Missouri in the 1950s and 1960s that capture sediment, and because of land use changes in the upper Mississippi and Ohio River valleys, contributions of the upper Mississippi and the Ohio Rivers are proportionally greater than they were in the 1700s (Meade, 1995). Figure 2-13 presents annual average estimates of Mississippi River suspended sediment loads at New Orleans for much of the twentieth cen- tury. The figure shows a steadily declining trend of suspended sediments in the river. It should be noted that estimates of suspended sediment yields and loads from the Mississippi River watershed vary among investigators because of variability in water discharge; length and completeness of the period of record; effects of variations of velocities with depth; logistical issues related to working in a large river; and sampling frequency (Meade, 1995; Turner and Rabalais, 2004). (mgL–1) FIGURE 2-13  Annual average suspended sediment concentrations in the Missis- sippi River at New Orleans, Louisiana. SOURCE: Reprinted, with permission, from data compiled by R. E. Turner, Louisi- ana State University. Data from New Orleans Sewage Board at Carrolton Treatment FIGURE 2-13 Plant, 1909-1993. Annual averages represent at least weekly, if not daily, measure- ments. All measurements were from gravimetric methods. 

48 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT As shown in Figure 2-12, sediment inputs to the lower Mississippi River historically have been dominated by Missouri River flows. Although pres- ent and historical suspended sediment data have some inconsistencies, the data starting about 1915-1920 began a more reliable period of suspended sediment measurements for the system and heralded a period of decline in suspended sediment. Dams for flood protection and to enhance navigation were constructed on the Ohio River and in the upper Mississippi basin, re- spectively, in the 1930s. Large dams also were constructed in the Tennessee basin (Wilson Dam at Muscle Shoals was completed in the 1920s; others followed in the 1930s after the Tennessee Valley Authority was established in 1933) and on the Missouri River (1950s and 1960s). The decrease in suspended sediments has occurred mostly since 1950, when the largest natural sources of sediments in the drainage basin were cut off from the Mississippi River mainstem by the construction of large storage dams on the Missouri and Arkansas Rivers (Meade and Parker, 1985; NRC, 2002). These dams trapped large amounts of sediments and altered transport pat- terns of suspended sediments downstream in the basin all the way to New Orleans and into the Gulf of Mexico (Meade et al., 1990). Present downstream sediment loads, however, may often be derived in considerable part from stream channel and bank erosion (Trimble, 1977, 1999). Sediment particles from current erosion may go into storage at the base of slopes or on downstream floodplains. Conversely, erosion of stream banks and channels may entrain sediment that may be anywhere from a few hours to a few millennia old. This situation is especially important in stream basins that have suffered heavy soil erosion in historical time, where many legacy sediments exist. Thus, downstream sediment yields may not reflect the quantity or the quality of material being currently eroded from slopes (Glanz, 1999; Trimble, 1976, 1977). As a result, current efforts to reduce soil erosion may be successful, but results often are not measurable downstream, at least in the short run. The effects of sediments and sedimentation on water quality and habi- tat are important issues along the upper Mississippi River and provide examples of excess sediment as a pollutant. The Minnesota River, for ex- ample, contributes a large amount of sediment to the Mississippi just below Minneapolis-St. Paul. The Minnesota River runs through agricultural land in southern Minnesota and transports large loads of nutrients, pathogens, pesticides, and sediments. A large portion of the Minnesota River sediments delivered to the upper Mississippi River is deposited in Lake Pepin (less than 50 kilometers downstream), resulting in the gradual filling of that large, natural river impoundment. In contrast to upper parts of the Mississippi River watershed where large amounts of sediments are input to the river and its floodplain and backwater areas, the deltaic plain of the Mississippi River is receiving less 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 49 sediment than it did historically. The 9,600 square mile deltaic plain was formed and sustained over the last 6,000 years by delta lobe switching, cre- vasses, river floods, storms, tides, and wetland plants (Penland et al., 1988). Wetlands across the coast survived for centuries after they received substan- tial inputs of river sediments. Before the construction of the numerous large levees along the lower Mississippi River, regular overbank flooding and cre- vasses maintained the river’s sediment input to the coastal landscape. The extensive tidal wetlands and other landforms of the Louisiana coast rapidly deteriorated with increased river control, particularly during the last half of the twentieth century. These changes have been driven by a variety of activi- ties. The closing of distributary channels and construction of artificial levees along the river limit the nourishment of wetlands with sediments and fresh water. The numerous canals across the Mississippi River delta that have been dredged for navigation, oil and gas production, and transportation, have caused widespread hydrological modifications. The delta region also experiences relatively high rates of subsidence; the reduction in sediments that could help compensate for these losses has contributed to the deterio- ration of barrier islands along the Louisiana coast (Boesch et al., 1994). Although some of these processes are natural, most of these environmental changes have been due to human activities that have disrupted river flows and altered hydrologic patterns. Most wetland losses in Louisiana have resulted from submergence, as accretion of new soil and organic plant mate- rial is unable to keep pace with the relative sea level rise because of altered hydrology, lack of mineral sediments, and deteriorated landscapes that do not support continued growth of marshes. More than 1,900 square miles of coastal land, mainly tidal wetlands, has been lost since the 1930s (Bar- ras, 2006). The annual rate of loss slowed from a peak of 40 square miles per year in the 1960s and 1970s to 24 square miles per year between 1990 and 2000. In addition to these trends, the land and water configuration of coastal Louisiana was dramatically affected by Hurricanes Katrina and Rita in 2005. Comparison of satellite imagery before and after the landfalls of these hurricanes showed that the water area in coastal Louisiana increased by roughly 217 square miles after their passage (Barras, 2006). Other Pollutants In addition to concerns about nutrients and sediments, there are many other Mississippi River water quality problems. For example, toxic sub- stances of major concern in the Mississippi River include metals (primarily mercury, zinc, and lead), organometallic compounds (primarily methylmer- cury and tributyltin), and a long list of toxic organic chemicals. Important among the latter are the chlorinated aromatic compounds (including PCBs), chlorinated hydrocarbons (including DDT, its degradation products, and 

50 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT other pesticides), and polycyclic aromatic hydrocarbons. Fecal bacteria also are an important water quality concern in areas of the mainstem Mississippi River. The distribution of all of these contaminants along the river depends on the nature and location of the source, their stability, their dilution by receiving waters, and their adsorption by sediments and the movement of these sediments. The U.S. Geological Survey (USGS) Mid-Continent Survey of con- taminants in the Mississippi River and some of its major tributaries was conducted from 1987 to 1990 and expanded in 1991-1992 to include sam- plings along the length of the river between Minneapolis-St. Paul and New Orleans (Meade, 1995), and provides a data-rich snapshot of conditions in the river. The survey focused on dissolved contaminants, those associated with the suspended sediments, and those stored in river bottom sediments in the upper Mississippi River. Much of the summary below is derived from this study and from the Meade (1995) synthesis volume. Metals Lead and other heavy metals are associated with suspended sediments along the length of the Mississippi River (Figure 2-14). Lead comes from both natural and human-related sources, but its sources in the upper Mis- sissippi River are mostly industrial and municipal. Lead in suspended sedi- ments tends to be most concentrated downstream of Minneapolis-St. Paul and also shows slight increases related to more concentrated inputs from the Ohio River. Lead at “moderately polluted” levels (40 micrograms per gram of sediment) occurs in bed sediments within the pools of the upper Mississippi River and is closely correlated with the finer clay fraction of sediments, but may also reflect the legacy of lead mining in some areas. An- other metal of environmental concern, mercury, has been found at concen- trations considerably lower than those of lead (Garbarino et al., 1995). Dissolved inorganic mercury (Figure 2-15) was lowest in the Mis- sissippi River’s upper reaches and gradually increased downriver. High concentrations were measured downstream of tributaries, such as the Des Moines, Illinois, and Missouri Rivers, and near large metropolitan and industrial centers, specifically St. Louis, Vicksburg, and below Baton Rouge. Concentrations of dissolved inorganic mercury decreased below these points, due to transformation to organic forms, adsorption onto sediments, or both. Mercury concentrations in sediments of pools in the upper Mississippi River were correlated with the organic content of the sediments, and except in Lake Pepin, most were not high enough to cause adverse toxicological effects. Mercury can bioaccumulate in many aquatic organisms, especially fish, through ingestion of suspended or bed-sediment particles. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 51 FIGURE 2-14  Lead in Mississippi River waters and sediments. SOURCE: Garbarino et al. (1995). Figure 2-14 PCBs Polychlorinated biphenyls are organic contaminants that were formerly used widely in industrial applications. Along the Mississippi River, they are typically most highly concentrated in suspended sediments near Minneapo- lis and St. Louis. Industrial activities in the Minneapolis-St. Paul region 

52 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT FIGURE 2-15  Mercury dissolved in Mississippi River water. SOURCE: Garbarino et al. (1995). Figure 2-15 led to PCB concentrations there that were five to ten times higher than in other parts of the river. Concentrations of PCBs were greatest in sediments between Minneapolis-St. Paul and Lake Pepin. Increased concentrations near St. Louis reflect the input of suspended sediments from the Ohio River, which usually contain more PCBs than do the waters in the middle reaches of the river. Hexachlorobenzene, another organic contaminant of industrial origin adsorbed to suspended sediments, is derived predominantly from the Ohio River and the industrial corridor along the lowermost 400 kilometers (248 miles) of the Mississippi River. There are hundreds of different kinds of PCBs, and numerous medical studies show that they have a variety of human health effects. In addition to the direct implications of PCBs for hu- man health, bioaccumulation of PCBs in fish tissue is another key concern in the Mississippi River (see Box 2-1). PCBs are legacy contaminants that are stored in bed sediments in the navigation pools of the upper Mississippi River. The concentrations in the upper (10 centimeters) sediments are high below Minneapolis-St. Paul, reach their highest values in Lake Pepin, and are significantly lower in the 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 53 BOX 2-1 Toxic Substances and Fish Contamination A key concern for commercial and recreational fishermen on the Mississippi River is the existence of toxic substances in the river’s fish populations. States along the Mississippi River issue various versions of fish consumption advisories, which are usually based on concentrations in fish tissue. Fish tend to accumulate long-lived, slightly soluble chemicals such as PCBs, pesticides, and herbicides in their fatty tissue. Concentrations of toxic substances in fish tissue can be much higher than in the water. Most of the 10 states along the mainstem Mississippi River list some reach as being of impaired water quality, and most of these impair- ments are based on fish tissues that contain unacceptable concentrations of toxic substances. For example, Illinois, Minnesota, Missouri, Tennessee, and Wisconsin list the entire river for PCBs; Tennessee lists dioxin and chlordane; and Minnesota and Wisconsin list mercury, all on the basis of high concentrations in fish. pools downriver of Lake Pepin (Rostad et al., 1994). After they were banned in 1977, concentrations of PCBs in the upper layers of bed sediments de- creased dramatically, especially in pools 2-9 (UMRCC, 2002). Evidence of the contaminant legacy, however, is seen in deeper buried sediments, where concentrations are much higher (Rostad et al., 1994). Chlordane concentra- tions also decreased, especially in pools 10-26 (UMRCC, 2002). Pesticides and Herbicides About two-thirds of all pesticides and herbicides used in U.S. agri- culture, most of which are used for weed control, are applied in the Mis- sissippi River basin (Goolsby and Pereira, 1995). Concentrations of 32 pesticides and herbicides and their degradation products have been found in Mississippi River water (Goolsby and Pereira, 1995); the most common is atrazine, a pre-emergent herbicide used mainly on cornfields. It is nearly ubiquitous along the river, with highest concentrations near St. Louis. It de- rives from the Missouri, Illinois, and other rivers that drain farming regions across the Corn Belt. Metolachlor, like atrazine, also was detected in more than 95 percent of the Goolsby and Pereira (1995) samples. Average annual concentrations of all pesticides and herbicides were far below the maximum contaminant levels for treated drinking water or health advisories, and only a few individual samples exceeded allowable levels of atrazine, alachlor, and cyanazine. Pesticide and herbicide concentrations are typically low during the summer, fall, and winter and then rise sharply in April and May as 

54 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT farmers apply them to fields for weed control and spring rains wash some of the chemicals off. Pesticide and herbicide concentrations then typically decline in June, depending on rainfall patterns. Unlike the legacy pollut- ants discussed earlier, most pesticides and herbicides in use today are water soluble and decay relatively rapidly. Fecal Bacteria Coliform bacteria are present in the fecal matter of all warm-blooded animals, including humans. Therefore, they are present in untreated or in- completely treated domestic sewage, animal waste (livestock, domestic and wild), and feedlot runoff. They have been used for nearly 100 years as an indicator of the possible presence of many pathogenic organisms that are too impractical to test for and quantify routinely. The only comprehensive collection of fecal coliform data for the entire Mississippi River is that compiled by the USGS for 1982-1992 (Barber et al., 1995; Figure 2-16). Those data indicated greatly improved water quality compared to levels measured in the preceding 80 years, although there were still high counts of fecal coliforms near and downstream of the Quad Cities (Bettendorf and Davenport, Iowa, and Moline and Rock Island, Illinois); below St. Louis and Cape Girardeau, Missouri; below Vicksburg, Mississippi; and below Baton Rouge and Belle Chasse, Louisiana. In Minnesota, the Twin Cities Metropolitan Council has effected major improvements in Mississippi River water quality with improved waste- water treatment since the 1960s. Since then, fecal coliform counts at St. Paul gradually have trended downward. Water quality improvement at Newport-Inver Grove, Minnesota, downstream from the main wastewater treatment plant, has been even more dramatic. As a result of these improve- ments, Minnesota now lists only 36 miles of the Mississippi River as hav- ing impaired water quality because of fecal coliforms in the vicinity of the Twin Cities, all upstream of the main wastewater treatment plant. Further downstream in Illinois, several areas along the Mississippi River have fecal coliform counts with annual averages lower than the standard, but Illinois lists the entire river along its border as being of impaired quality due to fe- cal coliforms because of high counts during storm runoff. In the Mississippi River below Baton Rouge, Louisiana, geometric means at five stations were lower in 1984-1995 than in 1977-1984 (Caffey et al., 2002). An average of 200 to 500 fecal coliform colonies per 100 milliliters characterized the Mis- sissippi River below Baton Rouge for 1982-1992 (Barber et al., 1995). The fact that fecal coliform counts at many locations along the river routinely average more than 200 CFU (colony-forming units) per 100 mil- liliters does not necessarily mean that wastewater treatment plants are not effective enough. There is general agreement today that the major remain- 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 55 Figure 2-16 FIGURE 2-16  Fecal coliform concentrations along the Mississippi River from 1982 to 1992 (U.S. Environmental Protection Agency, STORET database; U.S. Geologi- cal Survey WATSTORE database; Illinois River Watch; specific samples from the 1991-1992 USGS study). The bar-and-whisker plots represent the median and 10th, 25th, 70th, and 90th percentiles. SOURCE: Barber et al. (1995) (erratum resulted in this corrected Figure 53 from Barber et al., 1995). 

56 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT ing fecal coliform sources derive from urban and rural stormwater runoff, followed by combined sewer overflows (CSOs) from some large cities, and separate sanitary sewer overflows (SSOs) in some cities, during major rainstorms. Sewer overflows are considered point sources under the Clean Water Act and are being addressed by many cities, but correction is slow and expensive. However, stormwater runoff is more difficult to control. Emerging Contaminants New types of chemical and biological contaminants are the subject of exploratory monitoring. Examples of emerging contaminants include pharmaceuticals, fluorochemicals, and human-animal antibiotics and hor- mones (Kolpin et al., 2002; Field et al., 2006). Such compounds have been measured in the Mississippi River and its tributaries (e.g., Boyd and Grimm, 2001; Kolpin et al., 2002). Potential concerns related to these enti- ties include abnormal physiological processes and reproductive impairment, induction of cancer, development of antibiotic-resistant bacteria, and other effects. For many emerging contaminants, little is known about potential effects on humans and aquatic ecosystems, especially for long-term, low- level exposure, which is the typical scenario. WATER QUALITY IMPACTS IN THE GULF OF MEXICO The Mississippi River and its freshwater discharge, sediment delivery, and nutrient loads have strongly influenced the physical and biological processes in the adjacent Gulf of Mexico over geologic time and past cen- turies, and even more strongly during the last half of the twentieth century. As mentioned earlier, nutrient overenrichment in many areas around the world is having pervasive ecological effects on coastal ecosystems, includ- ing noxious (and possibly toxic) algal blooms, reduction in levels of dis- solved oxygen, and subsequent impacts on living resources (NRC, 2000a; Vitousek et al., 1997). The largest zone of oxygen-depleted coastal waters in the United States, and the entire western Atlantic Ocean, is found in the northern Gulf of Mexico on the Louisiana-Texas continental shelf (Rabalais et al., 2002b; examples for 2001 and 2002 are shown in Figure 2-17). The midsummer extent of bottom-water hypoxia (dissolved oxygen concentration less than 2 milligrams per liter) averages 12,900 square ki- lometers since systematic mapping began in 1985 and reached its maximal size to date of 22,000 square kilometers in 2002 (Rabalais and Turner, 2006; Figure 2-18). To appreciate the extent of these oxygen-depleted wa- ters, consider that the size of this hypoxic zone is as large as New Jersey or Rhode Island and Connecticut combined and, at its largest, is the size of Massachusetts. The distance across the hypoxic area that stretches from the 

Figure 2-17 FIGURE 2-17  Similar size and expanse of bottom-water hypoxia in mid-July 2002 (shaded area) and in mid-July 2001 (outlined 57 with dashed line). 

58 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT 20,000 5-year Average 15,000 Long-Term Average Area (km 2) 10,000 Action Plan Goal 5,000 1989 no data 0 1985 1986 1987 1988 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 FIGURE 2-18  Estimated bottom areal extent of hypoxia (dissolved oxygen <2 mg/L) for midsummer cruises and the 2015 goal of 5,000 km2 or less with long-term average sizes superimposed. Figure 2-18 SOURCE: Modified, with permission, from Rabalais et al. (2002a). © 2002 by The American Institute of Biological Sciences. Mississippi River across Louisiana’s coast and onto the upper Texas coast is comparable to the distance between Chicago and St. Louis or between Milwaukee and Minneapolis-St. Paul. The area affected by hypoxic, or low oxygen, conditions is commonly known as the Dead Zone because few marine animals can survive in these low oxygen concentrations (Rabalais and Turner, 2001). Swimming fish, crabs, and shrimp must escape or succumb to the low oxygen; other organ- isms eventually suffocate and die. The entire water column, however, is not devoid of oxygen, and fish survive in the upper waters along with hosts of bacteria at the seabed that can withstand low-oxygen conditions. Hypoxic conditions can damage fisheries and alter ecosystem functioning (Diaz and Rosenberg, 1995; Rabalais and Turner, 2001). Hypoxia, as a symptom of nutrient enrichment, is a growing problem around the world (Diaz and Rosenberg, 1995; Boesch, 2002; UNEP, 2006). The size and persistence of hypoxia on the Louisiana-Texas shelf, however, along with its connection to changes in Mississippi River nutrient delivery, make the Gulf of Mexico hypoxic zone a notable example. 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 59 Hypoxia is a seasonal but perennial feature of the coastal waters down- stream from the Mississippi River discharge and is most prevalent from late spring through late summer. Typical water depths for hypoxia are between 5 and 40 meters. Although hypoxia is commonly perceived as a bottom- water condition, oxygen-depleted waters often extend up into the lower one-half to two-thirds of the water column. The effects, therefore, extend past organisms and processes at the bottom and into a much larger volume of water across the Louisiana coast. The Mississippi River system is the dominant source of fresh water, sed- iments, and nutrients to the hypoxia zone in the northern Gulf of Mexico. The river carries 96 percent of annual freshwater discharge, 98.5 percent of total nitrogen, and 98 percent of total phosphorus load (calculated from U.S. Geological Survey streamflow data for 37 U.S. streams discharg- ing into the Gulf of Mexico; Dunn, 1996; Rabalais et al., 2002b). Direct deposition of nitrogen from rainfall on the area of hypoxia is minimal (1 percent) compared to the load delivered by the Mississippi River (Goolsby et al., 1999). The river constituents are carried predominantly westward along the Louisiana-Texas coast, especially during peak spring discharge. Although the area of the discharge’s influence is an open continental shelf, the magnitude of flow, ocean currents, and average 75-day residence time for fresh water result in an unbounded estuary, which is stratified for much of the year. This stratification is due primarily to salinity differences, and the stratification intensifies in summer with the warming of surface waters (Wiseman et al., 1997). Hypoxia is the result of the strong and persistent stratification coupled with the high phytoplankton growth in overlying surface waters that is fueled by river-derived nutrients (Rabalais and Turner, 2001; Rabalais et al., 2002a, 2002b). Nutrients delivered from the Missis- sippi River basin support phytoplankton growth in the immediate vicinity of the river discharges, as well as across the broader Louisiana and upper Texas coasts. The sinking of dead phytoplankton cells or the fecal pellets of zooplankton that have eaten phytoplankton to the lower water column and seabed provides a large carbon source for decomposition by oxygen- consuming bacteria. The bacterial decomposition process consumes dis- solved oxygen in the water column at a higher rate than resupply from the upper water column across the stratified water layers. Oxygen levels slowly decline over days to weeks, eventually becoming less than the 2 milligrams per liter that defines hypoxia and may approach conditions without oxygen (anoxia). The constituents of Mississippi River discharge changed substantially in the last half of the twentieth century, as outlined above. There is con- siderable evidence that nutrient-enhanced primary production, particularly by nitrate-nitrogen (nitrate-N), in the northern Gulf of Mexico is causally related to the oxygen depletion in the lower water column (CENR, 2000; 

60 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Justic et al., 2002; Rabalais et al., 2002a, 2002b; Turner et al., 2005, 2006). ´ For example, strong temporal linkages have been demonstrated among freshwater delivery, nitrate flux, high algal production in the surface waters (Justic et al., 1993; Lohrenz et al., 1997), and subsequent bottom-water ´ hypoxia (Justic et al., 1993). Models of a site within an area of persistent ´ hypoxia about 100 kilometers west of the Mississippi River clearly link nitrate flux from the Mississippi River with both surface and bottom-water oxygen conditions (Justic et al., 1996, 2002). Other models have been used ´ to predict oxygen conditions retroactively on the Louisiana coast to the early 1950s when nitrate data became readily available; all results show a decrease in bottom-water oxygen levels in the early 1970s (Scavia et al., 2003; Turner et al., 2005, 2006). These models effectively link nitrate loads from the Mississippi River with the bottom area size of the hypoxic zone in midsummer. Data showing oxygen concentrations on the Louisiana coast indicate a gradual decline in bottom-water oxygen levels across the coast for the periods of record (1982-2002 and 1978-1995; see Stow et al., 2005; Turner et al., 2005). A model developed by Turner et al. (2006) tests the relationship of hypoxic area size to factors such as other forms of nitrogen, phosphorus, dissolved silicate, and their concentration ratios. In this model, the strongest relationship was found with nitrate. To understand conditions on the Louisiana coast for periods in which actual oxygen measurements do not exist, chemical and biological indicators in sediments where hypoxia is now a persistent condition were examined. The accumulated evidence in sediments shows trends of increased phyto- plankton production in the last half of the twentieth century accompanied by more severe or persistent hypoxia beginning in the 1960s to 1970s and becoming most pronounced in the 1990s (Rabalais et al., 2007). The shifts in sediment indicators are temporally consistent with the rise in Mississippi River nitrate levels and with modeling results. Specific indicators demon- strate increased accumulation of phytoplankton biomass—stable carbon isotopes, silica, remains of diatoms, the abundance of a specific diatom that can generate harmful toxic substances, and specific phytoplankton pig- ments. These trends show that while there are signs of increased production and oxygen depletion earlier in the twentieth century, the most dramatic changes have occurred since the 1960s, when the nitrate concentration and load from the Mississippi River began to increase. Hypoxia in the northern Gulf of Mexico occurs in an important com- mercial and recreational fisheries zone that accounts for 25 to 30 percent of the annual coastal fisheries landings for the United States. The ability of organisms to live, or even survive, either at the bottom or within the hypoxic water column is severely affected as the depletion of oxygen pro- gresses toward anoxia. When the dissolved oxygen content is less than 2 milligrams per liter, animals capable of swimming evacuate the area. Less 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 61 motile animals living in the sediments experience stress or die as oxygen concentrations fall to zero. The abundance of animals in the sediment and the diversity of the sediment-dwelling community are severely reduced, which means less food and less preferred food for the shrimp and fish that depend on them. Numerous studies document the effects of hypoxia on coastal fish and shrimp. Shrimp, as well as the dominant fish, the Atlantic croaker, are absent from the large areas affected by hypoxia (Renaud, 1986; Craig and Crowder, 2005; Craig et al., 2005). There is a negative relation- ship between the catch of brown shrimp—the largest economic fishery in the northern Gulf of Mexico—and the relative size of the midsummer hypoxic zone (Zimmerman and Nance, 2001). The catch per unit effort of brown shrimp declined during a recent interval in which hypoxia was known to expand (Downing et al., 1999). The presence of a large hypoxic water mass when juvenile brown shrimp are migrating from coastal marshes to offshore waters inhibits their growth to a larger size and thus affects the poundage of captured shrimp (Zimmerman and Nance, 2001). The unavailability of suitable habitat for shrimp and croaker forces them into the warmest waters inshore and also cooler waters offshore of the hypoxic zone with potential effects on growth, trophic interactions, and reproduc- tive capacity (Craig and Crowder, 2005). The overall implications of these indirect stressors for the Gulf of Mexico fisheries production and its overall productivity are not fully known. There have been no catastrophic losses of fishery resources in the northern Gulf of Mexico. In fact, the abundance of some pelagic components, which have greater volume but less economic value, has increased. This has been to the detriment of bottom-dwelling animals (Chesney and Baltz, 2001). Several different initiatives have been taken to help address the problem of hypoxia on the Louisiana coastal shelf. For example, the Action Plan for Reducing, Mitigating, and Controlling Hypoxia in the Northern Gulf of Mexico (USEPA, 2001) was endorsed by federal agencies, states, and tribal governments. The action plan calls for a long-term adaptive management strategy that couples management actions with enhanced monitoring, mod- eling, and research. Implementation will depend on a series of voluntary and incentive-based activities, designed within a series of subbasin strate- gies, including best management practices on agricultural lands, wetland restoration and creation, river hydrology remediation and riparian buffer strips, and stormwater and wastewater nutrient removal (Mitsch et al., 2001). These subbasin efforts, which are intended to achieve a nitrogen load reduction of 30 percent, will work toward a goal of a Gulf of Mexico hypoxic zone smaller than 5,000 square kilometers (five-year running av- erage) by the year 2015. Some modeling studies, however, suggest that a greater reduction—35 to 45 percent—in the nitrogen load will be required to meet this goal (Justic et al., 2003; Scavia et al., 2003). In 2006, five years ´ 

62 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT after its adoption, the action plan was being reassessed with regard to new scientific knowledge and management scenarios. Despite the plan and the activities begun in connection with it, in the last five years little change has been implemented within the watershed, and the size and persistence of the hypoxic area continue unabated. SUMMARY The Mississippi River basin covers nearly one-half of the continental United States and exhibits a variety of landforms, landscapes, climate zones, and land uses. There are natural differences in these features across the wa- tershed, and there have been extensive human-induced changes in land uses and Mississippi River hydrology. Huge swaths of forested lands and prairie have been converted to cropland; numerous locks and dams have been constructed on the upper Mississippi, Missouri, and Illinois Rivers; most of the natural wetlands along the length of the river and in the watershed have been drained and converted to other uses; and huge levees for both flood protection and navigation purposes have been constructed along the lower Mississippi River. The primary land use across the basin today is ag- riculture. With regard to human population, many parts of the Mississippi River basin are lightly populated in comparison with the more urbanized U.S. East and West Coasts, and urban areas constitute only a small per- centage of total land use in the basin. Population in all the basin states is growing; while some rural areas are experiencing population declines, some urban areas are growing rapidly. Differences in natural features across the river basin, coupled with two centuries of anthropogenic changes in land cover, land uses, and the construction of river control structures, influence both the amount of Mississippi River discharge and its constituents and pollutants, such as nutrients, suspended sediments and other particulate materials, and toxic chemicals. In terms of Mississippi River hydrology and sediment transport, the river exhibits a very different character in its various reaches. The upper and lower Mississippi Rivers are, in fact, in many ways two different river systems. For example, many portions of the upper Mississippi River contain islands and large backwater areas important to recreational activities such as boating, fishing, and trapping, and they share the river, its channel, and its numerous navigation pools with commercial navigation. By contrast, the lower Mississippi River below Cairo, Illinois, contains fewer islands and is leveed off from most of its previous floodplain areas. The lower Missis- sippi River carries much larger river flows and poses dangers that inhibit recreational boating, fishing, and related activities. Levels of sediment transported by the Mississippi River and its tributar- ies have changed greatly since the 1700s. In particular, whereas the Mis- 

CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 63 souri River once delivered huge quantities of sediment into the Mississippi River, construction of storage dams on the Missouri River in the 1950s and 1960s greatly reduced these inputs. The total amount of sediment car- ried by the Mississippi River and delivered to the Gulf of Mexico has been reduced significantly. The depletion of this sediment, among other natural and human activities, has led to the loss of many wetlands and coastal bar- riers in coastal Louisiana and other areas along the U.S. Gulf Coast. The upper Mississippi River today carries a proportionally greater amount of the river’s total sediment load than in 1700, and sedimentation is a problem in many areas of the upper Mississippi River, both in the main channel and in backwater areas. Highest inputs and concentrations of nutrients are in the upper and middle reaches of the Mississippi River. Uptake and transformation of nutrients is more likely to occur closer to the sources and in the smaller streams. Once nutrients reach the mainstem, there is little loss or dilution on the way to the river delta—an important point to be considered in nutri- ent management efforts. Excess nutrient input to the Mississippi River, in various forms of dis- solved and particulate nitrogen and phosphorus, causes significant water quality problems both within the Mississippi River itself and in the coastal waters of the northern Gulf of Mexico. These latter problems manifest themselves as Gulf of Mexico hypoxia, one of the nation’s prominent regional-scale water quality problems. Nutrient enrichment, primarily from dissolved inorganic nitrogen, causes disturbance of the coastal ecosystem including, but not limited to, hypoxia, noxious and toxic algal blooms, impacts on living resources, and fishery impacts. The importance of phos- phorus as a limiting nutrient to phytoplankton growth is more evident in the spring and in the upper Mississippi River. Given the importance of both nitrogen and phosphorus in various forms, it is necessary to consider management of both of these nutrient inputs, which stem primarily from nonpoint sources. These activities and modifications contribute to water quality problems along the river’s mainstem that are numerous, variable in nature, and of different magnitudes in different parts of the river. These problems can be divided into three broad categories: (1) contaminants with increasing inputs along the river that accumulate and increase in concentration downriver from their sources (e.g., nutrients and some fertilizers and pesticides); (2) legacy contaminants stored in the riverine system, including contaminants adsorbed onto sediment and stored in fish tissue (e.g., PCBs and DDT); and (3) “intermittent” water constituents that can be considered contaminants or not, depending on where they are found in the system, at what levels they exist, and whether they are transporting adsorbed materials that are contaminants. The most prominent component in the latter category is 

64 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT sediment. In some portions of the river system, sediment is overly abundant and for that reason can be considered a contaminant. In other places it is considered a natural resource in deficient supply. At the scale of the entire Mississippi River, including its effects that extend into the northern Gulf of Mexico, nutrients and sediment are the two primary water quality problems. Nutrients are causing significant wa- ter quality problems within the Mississippi River itself and in the northern Gulf of Mexico. With regard to sediment, many areas of the upper Mis- sissippi River main channel and its backwaters are experiencing excess sediment loads and deposition, while limited sediment replenishment is a crucial problem along the lower Mississippi River and into the northern Gulf of Mexico. Nutrients and sediments from nonpoint sources are the primary water quality problems focused on in this report. With respect to nutrients and sediments (and some toxic substances), water quality in the lower Mississippi River is determined largely by inputs in the upper Missis- sippi River basin, with different portions of the upper river basin having a dominant influence for particular constituents. For example, sediment loads are determined largely by the Missouri River contributions, and nutrient contributions are primarily from the upper Mississippi River. In addition to nutrient and sediment issues, the Mississippi River has a variety of other water quality challenges. Toxic substances, including PCBs, metals, and pesticides, have important human health implications and are related primarily to legacy inputs. Their concentrations, fortunately, have been decreasing with time, in large part due to reductions in point source contributions as a result of the Clean Water Act. Similarly, the Clean Water Act has been useful in substantially reducing fecal coliform levels in the Mississippi River. The Clean Water Act was designed to remediate some of the impacts of human activities and has been effective in reducing many impacts attributable to point sources. Many of today’s water quality prob- lems, however, are nonpoint in nature. Whereas the Clean Water Act has been successful in reducing many point source pollution problems along the Mississippi River, it has not been as successful in reducing nonpoint source pollutants. Both the source and the scale of Mississippi River and Gulf of Mexico nonpoint source water quality problems pose significant Clean Water Act-related manage- ment challenges. The following chapters describe the Clean Water Act and discuss challenges in its administration to achieve its goals of attaining fishable and swimmable water quality and restoring the chemical, physi- cal, and biological integrity of water resources as these goals apply to the Mississippi River.