2
Characteristics of the Mississippi River System

The 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 covers 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 Appalachian 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; approximately 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 Mississippi 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 pallid sturgeon and several mussels. The Mississippi River, particularly in its upper reaches, has important commercial and recreational fisheries; the Upper Mississippi River National Wildlife and Fish Refuge hosts an estimated



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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 

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 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.

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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.

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 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.

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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

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 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

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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).1 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 1 Midwesternstates listed in this category include Illinois, Indiana, Iowa, Kansas, Michigan, Minnesota, Missouri, Nebraska, North Dakota, Ohio, South Dakota, and Wisconsin.

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 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).

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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

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0 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,

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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).

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 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-

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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).

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 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

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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  with dashed line).

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 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT 20,000 5-year Average Long-Term 15,000 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.

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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;

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0 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

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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 ´

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 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-

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 CHARACTERISTICS OF THE MISSISSIPPI RIVER SYSTEM 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

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 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.