2
Changes in Missouri River Sediment and Related Processes

The Missouri River drains an area of 530,000 square miles and extends over one-sixth of the conterminous United States. The Missouri River originates at the confluence of the Gallatin, Jefferson, and Madison rivers near Three Forks, Montana, and then flows east and south to its confluence with the Mississippi River just upstream of St. Louis. Along its course, tributary streams such as the Yellowstone, Platte, and Kansas rivers flow into mainstem Missouri River. The basin exhibits a great diversity of landforms and terrain. Because of these differences, sediment loadings into the river and its tributaries vary greatly across the basin. Areas in the Rocky Mountains, for example, contribute only a small portion of the river’s total sediment load. The Sand Hills of central Nebraska, the Loess Hills of extreme western Iowa and northeastern Nebraska, and other areas of the northern Great Plains supply disproportionately large amounts of sediments to the Missouri River.

Before construction of mainstem dams and extensive river-training structures in the twentieth century, the Missouri River was a major contributor of sediments to the Mississippi River, which transported portions of these sediments downstream and to the Gulf of Mexico. Before 1900, the Missouri and lower Mississippi river system transported an estimated 400 million metric tons per year of sediment from the interior United States to coastal Louisiana (Meade and Moody, 2009). Approximately 300 million tons were transported by the Missouri River past Hermann, Missouri (Jacobson et al., 2009).



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2 Changes in Missouri River Sediment and Related Processes T he Missouri River drains an area of 530,000 square miles and ex- tends over one-sixth of the conterminous United States. The Mis- souri River originates at the confluence of the Gallatin, Jefferson, and Madison rivers near Three Forks, Montana, and then flows east and south to its confluence with the Mississippi River just upstream of St. Louis. Along its course, tributary streams such as the Yellowstone, Platte, and Kansas rivers flow into mainstem Missouri River. The basin exhibits a great diversity of landforms and terrain. Because of these differences, sediment loadings into the river and its tributaries vary greatly across the basin. Ar- eas in the Rocky Mountains, for example, contribute only a small portion of the river’s total sediment load. The Sand Hills of central Nebraska, the Loess Hills of extreme western Iowa and northeastern Nebraska, and other areas of the northern Great Plains supply disproportionately large amounts of sediments to the Missouri River. Before construction of mainstem dams and extensive river-training structures in the twentieth century, the Missouri River was a major con- tributor of sediments to the Mississippi River, which transported portions of these sediments downstream and to the Gulf of Mexico. Before 1900, the Missouri and lower Mississippi river system transported an estimated 400 million metric tons per year of sediment from the interior United States to coastal Louisiana (Meade and Moody, 2009). Approximately 300 mil- lion tons were transported by the Missouri River past Hermann, Missouri (Jacobson et al., 2009). 19

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20 MiSSOuRi RivER PlANNiNg In the mid-twentieth century, six large dams were constructed on the river’s mainstem in Montana, North Dakota, and South Dakota. Hundreds of miles of river training structures also were built along the river between Sioux City, Iowa, and St. Louis. These structures were authorized by the U.S. Congress and were built to jointly facilitate navigation, control flood- ing, provide water supplies, and meet other social and economic needs. The large dams were built under the 1944 Pick-Sloan Plan, while many of the bank stabilization and channelization projects were built under the 1945 Bank Stabilization and Navigation Project (BSNP). These projects, along with changes to land cover and land use across the basin, had substantial influence on the Missouri River’s form, dynamics, and sediment regime. Current volumes of sediment transported into Louisiana by the Missouri and Mississippi rivers average roughly 145 million metric tons per year, of which only 55 million tons now pass Hermann, Missouri (Meade and Moody, 2009). This chapter discusses the importance and the roles of sediment in the Missouri River system. It reviews some fundamentals of sediment erosion, transport, and deposition and how these dynamics affected Missouri River landforms and structure. The chapter also reviews prominent sediment- related changes along the Missouri River during the twentieth century. These changes are strongly linked with changes to river hydrology during the same period, but consistent with this report’s statement of task, the emphasis is on sediment and sedimentary processes. The consequences of these major changes in sedimentary processes for ecology, water quality, and infrastructure, also are discussed. The relevance of sedimentary processes for current and future river management decisions, and the importance of the systematic collection, analysis, and evaluation of sediment data to underpin those decisions, also are examined. In fact, after two to three decades of being underappreci- ated as compared with Missouri River hydrology and water management, sedimentary processes now are seen as integral to twenty-first-century river basin management and merit wider attention and understanding. This chapter also comments on the value of more systematic, comprehensive, and easily accessible sediment data to support future river management decisions and actions. In addressing these topics, this chapter addresses two questions from this report’s 7-point statement of task: (1) How and why is sediment a significant variable in the environmen- tal restoration of a river system like the Missouri? (Question 1), and (2) Are there long-term consequences to the lack of sediment in the system to the human environment, either environmentally or economically? (Question 5).

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21 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES SOURCES OF MISSOURI RIVER SEDIMENTS The Missouri River has transported large volumes of sediment down- stream since at least the last Ice Age, roughly 18,000 years ago. Once the great continental ice sheets had melted and the bulk of their morainal de- posits washed downriver, shales and siltstones that lay under portions of the northern Great Plains yielded the largest quantities of fine-grained sediment delivered to the tributary streams of the Missouri River system. A combi- nation of highly erodible soils and low-to-moderate precipitation resulted in large natural yields of fine sediment being delivered to the mainstem Missouri River (Langbein and Schumm, 1958). Meanwhile, the remaining glaciofluvial materials, plus other coarser sediments derived from tributaries draining areas such as the Sand Hills of Nebraska, formed a broad flood plain that in some stretches was several miles wide. This coarser floodplain sediment was gradually being shifted downvalley through a combination of bank erosion and bar deposition. The Missouri River historically received eroded sediment from several tributary streams including the Yellowstone, Niobrara, James, Platte, and Kansas rivers. Some of these tributaries drain highly erodible areas (e.g., the Sand Hills) and areas of loess (wind-deposited silt) in northeastern Nebraska and western Iowa. In their travels along the Missouri River in 1804-1806, Lewis and Clark were the first to point out that the northern Great Plains, rather than the Rocky Mountains, are the source areas of large sediment loads to the river (Moody et al., 2003). Other tributaries (e.g., the Yellowstone) drain areas of relatively resistant bedrock and thus have historically been characterized by low turbidities and low sediment yields, supporting species and ecosystems adapted to clear water. This is in contrast to native species, such as the pallid sturgeon, which favor the highly turbid conditions in the mainstem Missouri River and some tribu- taries. Because different sediment grain sizes function differently through- out a river system, the diversity of these source regions plays an important role in shaping sediment fluxes and dynamics along the length of the Mis- souri River. Between the last Ice Age and about A.D. 1950, large quantities of sediment were transported into the Mississippi River and eventually to the Mississippi delta at the Gulf of Mexico. The transport processes were episodic, carrying some sediment particles only short distances each runoff season, storing the particles on the channel bed or in the floodplain during falling-water stages, and resuspending stored particles as the river waters rose again during subsequent seasons. More than half of the sedimentary materials that make up the multi-lobed delta that the Mississippi River was deposited on the shores of the Gulf of Mexico during the last 6,000-7,000 years (Blum and Roberts, 2009; Kolb and Van Lopik, 1958; Törnqvist et

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22 MiSSOuRi RivER PlANNiNg al., 1996) were “muds”—mainly silt and clay—derived ultimately from the Missouri River basin. Sediment yields from land encompassed by the Missouri River drainage basin have undergone dramatic and complex changes through settlement and subsequent development. Cropland agriculture was the first of the large human-caused alterations to this millennial-scale pattern of sediment deliv- ery from the Missouri River basin to the Mississippi River and the Gulf of Mexico. This extensive landscape alteration caused greater soil erosion and an increase in river-borne sediment. The most dramatic of these increases in the Missouri River basin were in southwestern Iowa and northwestern Missouri, where the highly erodible soils developed on the extensive loess deposits were exposed to erosion when their soils were plowed (Piest and Spomer, 1968; Piest and Ziemnicki, 1979). The introduction of modern conservation-oriented farming practices reduced the loss of sediment from cultivated fields, and improved grazing management reduced sediment pro- duced from pasture lands. Beginning in the 1930s, the efforts of the U.S. Soil Conservation Service and the effects of the Taylor Grazing Act of 1934 resulted in reduced contributions of upland sediment to the regional rivers (Branson et al., 1981). The geographic pattern of these sediment sources provides a template for understanding what would constitute a relatively natural and beneficial use reference condition when establishing water qual- ity standards for individual reaches of the river and its tributaries (the topic of reference condition is discussed further in Chapter 6). SEDIMENT EROSION, TRANSPORT, AND DEPOSITION Characteristics of Sediment Movement Sediment transported by large rivers includes a variety of sizes, rang- ing from clay (particles less than 4 microns in diameter), to silt (4 to 62 micrometers), to sand (62 micrometers to 2 millimeters), and gravel (2 to 64 millimeters). The rate of travel of sediment, its roles in affecting chan- nel behavior and water quality, and the degree to which sediments and associated particles are exchanged with floodplains, depend on the mode of particle transport. These modes, in turn, depend on sediment grain size and the depth and slope of the river. For example, in rivers like Missouri and Mississippi that experience sharp changes in seasonal water tempera- ture, changes in temperature-modulated viscosity of river water also affect the mode of sediment transport. Coarser particles are transported along or close to the channel bed, while fine particles are carried higher in the water column, which allows fine particles to more frequently enter the floodplain, chutes, and other waterbodies off the main channel. Finer particles are also washed downstream relatively rapidly and dominate the formation and

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23 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES maintenance of coastal wetlands where the Mississippi River sediment load enters the Gulf of Mexico. In contrast, the coarser sedimentary load is more important for shaping channel morphology, including channel bars that are important for native biota, some of them federally listed as threatened or endangered. Sediment particles on the riverbed are referred to as the bed-material load of the river. Transported particles that are finer than those found on the bed are referred to as washload (left side of Figure 2-1). This distinction varies somewhat as discharge changes throughout the year, but since most sediment is transported in floods, this report is concerned primarily with the flows near and above bankfull stage. Washload (clay, silt, and some fine sand in the case of the Missouri) is so fine that it travels continually suspended in turbulent flow and is rarely deposited within the active streambed, although it may settle out in over- bank flow and shallow water habitats at channel margins. The fraction of washload is the primary determinant of turbidity and of the capacity of the sediment to transport adsorbed chemicals, including phosphate and met- als. It is also a large contributor to the formation of floodplain habitats far from the main channel and of coastal deltaic areas. Measured suspended loads (upper right of Figure 2-1) include both washload and larger particles (dominantly sands) that are lifted into suspension from riverbeds during floods. This latter component is called the suspendible bed-material load (center of Figure 2-1) and it settles from suspension onto the channel bed FIGURE 2-1 Grain-size-dependent transport mechanisms and their relationships to Figure 2-1.eps measured sediment loads. bitmap

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24 MiSSOuRi RivER PlANNiNg and bars, or on the floodplain as flow velocities decline. Bedload particles, consisting of coarser sand and some gravel in the case of the Missouri, move along or at least within centimeters of the channel bed by rolling, sliding, and bouncing. Together, the bedload and the suspendible bed-material load constitute the bed material out of which the channel margin and its assorted bars and habitat features are constructed. The various modes of sediment transport affect its rate of travel, role in affecting channel form and behavior, habitat formation on bars and flood- plains, turbidity, chemical transport aspects of water quality, and the degree to which sediment and associated chemicals can be exchanged with the floodplain. In most lowland rivers, the bedload constitutes less than 5 per- cent of the total sedimentary load. However, bedload is a dominant control on channel morphology, navigability, and bar habitat to a degree that is far beyond its volumetric contribution to the total load. The geography of the river basin, and the engineering activities across the basin, create a supply of sediment with a certain grain size composition. The texture-modulated modes of transport are critical links between sediment supply and its roles in water quality and in habitat formation. Chemical and Nutrient Loads Streams and rivers also transport a variety of natural and human- affected chemical constituents along with sediment. A river’s chemical char- acteristics, as well as sediment grain sizes, are influenced by geology and soils, topography, hydrology, ecosystem processes, climate, and anthropo- genic influences. As river systems are dammed, channelized, and otherwise affected by human activities, there typically are changes to the stream’s chemical load. Two nutrients of concern in the Missouri and Mississippi river basins today are phosphorus (P) and nitrogen (N). These nutrients are vital for biological growth and are ubiquitous in natural waters and sediment. If other factors, such as light and turbidity, are not limiting, the levels of these nutrients have major effects on aquatic life. The various chemical forms of phosphorus and nitrogen behave dif- ferently in aquatic environments. In particular, nitrogen is more abundant in dissolved forms, whereas phosphorus is largely present in particulate forms (either adsorbed or as a constituent of inorganic and organic par- ticles). Common dissolved forms of nitrogen (such as nitrate) are not particle-reactive; in contrast, dissolved forms of phosphorus (such as phosphate) are particle-reactive and readily adsorbed by sediment. As a result, there is a strong correlation between suspended sediment and total phosphorus concentrations, and changes to the river system that alter the flow of water or sediment in the system are likely to cause a larger

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25 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES change in the concentration and transport of phosphorus than of nitrogen (Wetzel, 2001). The delivery of large volumes of nutrients from the Mississippi River basin to the Gulf of Mexico, and associated hypoxia in deeper waters of the Gulf, are prominent national water quality concerns. Analyses of river flows and concentrations have been used to estimate of loads of phosphorus and nitrogen from each of the major tributaries of the Mississippi River (Alex- ander et al., 2008; USEPA, 2007). Based on what is commonly understood about the sediment association of phosphorus, current and future projects for sediment regime restoration in the Missouri River may increase phos- phorus supply to the Mississippi. From a broader historical perspective, since the Missouri River always has carried a tremendous sediment load, and since natural suspended sediments carry a certain amount of phospho- rus, the preanthropogenic river thus likely carried significant phosphorus loads into the Mississippi River. However, it is not known what portion of these phosphorus loads reached the Gulf, were trapped in coastal wetlands, or were captured further upstream in the system. Roles of Sediment in Large River Systems The Missouri River’s native fish and bird species evolved in environ- ments with high turbidity, large volumes of mobile sediment, and hydrogeo- morphic conditions consistent with a sediment-rich river. In contrast, many other rivers and streams nationwide, including some Missouri River tribu- taries, naturally contain far lower concentrations of sediment. The sediment management challenges posed by varying concentrations of sediment across a river basin were noted in a Geological Society of America compilation of papers on river system management and human impacts: To many environmental scientists—such as those concerned with total maximum daily loads (TMDLs)—all sediment is treated as a pollutant. This perspective is in conflict with the need to introduce sediment to sediment-starved reaches below impoundments or where coarse sediment needs to be recruited to replenish spawning gravels on riffles and bars (James et al., 2009). On so-called “clear-water” streams and rivers, excess inputs of sedi- ment—for example from basin land uses such as agriculture or localized ac- tivities such as construction—can raise sediment concentrations in the water far higher than natural background or historical levels. In these cases, sedi- ment rightly can be viewed as a pollutant, with potentially severe impacts on species native to that tributary, to aesthetics, and to river form and water quality. In the Missouri River basin, however—in which preanthropogenic concentrations of sediment in reaches of the mainstem and some tributary

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26 MiSSOuRi RivER PlANNiNg streams were greater than those found in the river today—the designation of sediment as a “pollutant” is fraught with ambiguity (Chapter 6 contains further discussion of this topic). HYDROLOGIC AND GEOMORPHIC CHANGES TO THE MISSOURI RIVER Over long reaches of the Missouri River, hydrodynamic and geomor- phic processes have changed considerably over the past century. Dams, levees, dikes, and revetments have been constructed and now are operated to facilitate services such as transportation of bulk commodities through commercial navigation, flood protection for farms and cities, reliable water supply, hydropower generation, and water-related recreation. This section describes key historical changes to the Missouri River, with an emphasis on changes to or relevance of sedimentary processes for the preregulation Missouri River, the postregulation Missouri River, and changes to Missouri River ecology. The Preregulation Missouri River Early accounts of the Missouri River date back to Lewis and Clark and the expedition of their Corps of Discovery in 1804-1806, in which they made numerous entries in their journals about hydrology, turbidity, and river morphology. As the Great Plains were subsequently explored and settled, many observations and written accounts helped to produce an early picture of the river’s morphology and character.1 The preregulation Missouri River assumed different morphologies in different reaches of the river. In many stretches, the preregulation Mis- souri River was a multichannel system, with a primary channel and often multiple secondary channels (called “chutes” on the Missouri River), wide- spread bars, islands, and shallow sloughs (Hallberg et al., 1979; Moody et al., 2003). The river also featured natural levees, backwater lakes, large meander loops, oxbow lakes, and sandbars and dunes (Figure 2-2). Width of the main river channel was highly variable, ranging from roughly 1,000 to 10,000 feet during normal flow periods to 25,000 to 35,000 feet dur- ing floods (Schneiders, 1999). In some areas during large floods, the river flowed bluff-to-bluff and covered a width up to 17 miles (see NRC, 2002, for additional description of the preregulation Missouri River). Early ac- counts also described near-ubiquitous woody debris, or “snags” in the channel, present at all times and mobile during floods (Figure 2-3). These 1For more information on these topics, the interested reader is encouraged to consult Ambrose, 1997; Ferrell, 1993; NRC, 2002; and Schneiders, 1999.

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27 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES FIGURE 2-2 Idealized cross-section of a large river-floodplain ecosystem. Before extensive twentieth-century regulation, the Missouri River resembled this diagram Figure 2-2.eps in some reaches. In other reaches, the Missouri did not have a single, distinct river bitmap channel and assumed a more braided, multitributary character. SOURCE: Jacobson et al., 2007. snags derived primarily from riverbank erosion, a process that moved trees and other organic material from the floodplain surface into the channel. Vegetation along the Missouri River corridor was dense, with sandy low- water flats along the channel margin, stabilized by thickets of young wil- lows and cottonwood, and large forest trees on islands and the floodplain (Johnson, 1992; Schneiders, 1999). The processes of river bank erosion and lateral migration of the river channel were prominent in the preregulation Missouri River. In areas where the Missouri River channels migrated back and forth across the floodplain, river banks and sediment were eroded on the outside banks of mobile bends, while sediments were deposited on the bends’ inside edges, or on mid-channel bars where young vegetation slows flow and scavanges sedi- ment (Johnson, 2000). These processes played important ecological roles in the preregulation Missouri (Johnson et al., 1976; Johnson, 1992). The over- all sediment regime was one of intermittent transport, with some sediments stored for decades or centuries in bars or the floodplain, then remobilized by flood events (NRC, 2002; Slizeski et al., 1982). As a channel’s location changed through the processes of erosion and sedimentation, diversity developed in the riparian vegetation as distance from the present channel increased (Figure 2-4). Channel migration eroded older, well-established vegetation on the outside of river curves, while new bars on the inside of river curves were suitable for pioneer vegetation communities such as cot-

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28 MiSSOuRi RivER PlANNiNg FIGURE 2-3 Numerous “snags” characteristic of the preregulation Missouri River. SOURCE: Karl Bodmer, Swiss, 1809-1893, Snags on the Missouri, near the mouth of the Nemaha River. Watercolor and pencil on paper. Reprinted, with permission, from Joslyn Art Museum, Omaha, Nebraska: Gift of the Enron Art Foundation, 1986 (JAM 1986.49.150). tonwood and willow. Channel migration also contributed to floodplain species biodiversity by creating a mix of landforms such as oxbow lakes, sloughs, and backwater swamps with differing soil textures, chemistry, and inundation regimes. Distribution of riparian vegetation was also heterogeneous because tree species differ in their tolerances to flooding, sedimentation, and physical dam- age from floodwaters and debris (Hupp, 1988). Channel widening and lateral migration removed both living and dead trees from eroding banks, and many of these collected in the channel after floodwaters receded. This large woody debris (i.e., “snags”) contributed submerged substrate for invertebrates that are consumed by fishes and other vertebrates. Woody debris also provided cover for fish and contributed hydraulic roughness to the riverbed that locally modified channel bed texture, bathymetry, water depth, and organic matter distribution (Gurnell et al., 2002; Sedell and Froggatt, 1984).

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29 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES FIGURE 2-4 Model of lateral channel movement; accumulation of sediment on the Figure 2-4.eps inside (right side, above) of a channel bend; and seed dispersal, germination, and bitmap establishment. SOURCE: Reprinted, with permission, from Braatne et al., 1996. © 1996 by NRC Research Press. Riparian vegetation stabilized riverbanks and sandbars and slowed bank erosion and channel migration rates (Gran and Paola, 2001; McKenny et al., 1995). The presence of vegetation exerted a strong physical presence on floodplains by increasing surface roughness, reducing flow velocity, and capturing sediment from flood waters. Early-successional trees established on low sandbars near mean river level trapped and immobilized sediment up to 5 to 6 meters in depth (Johnson et al., 1976; Scott et al., 1997). The river’s sandbars and associated biotic communities are important habitat for many native riparian species whose life cycles and populations depended on the existence of the bars, as well as their continuing movement. Oc- casional shifting and movement of sandbars and other riparian landforms made long-term colonization by vegetation difficult, and the absence of vegetation made it difficult for predators to prey upon the nests of sandbar- nesting birds (Johnson, 2000; Osterkamp and Hedman, 1982). Floods were common and widespread on the preregulation Missouri. Floods allowed for the redistribution of sediment between the river’s main channel and its floodplains. As Missouri River flows increased during the spring, the river would erode sediment from its bed and its banks. Over- bank flows allowed the main channel to connect to backwater areas, allow-

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40 MiSSOuRi RivER PlANNiNg that about 175 million tons per year was supplied to the Missouri River mainly by large right-bank tributaries such as the Platte and Kansas rivers and, to a lesser extent, by left-bank tributaries (such as the Nishnabotna River) draining loess lands. Since this period also witnessed continuing engineering projects to se- quester sediment within the floodplain and stabilize the channel, tributary streams must have been supplying more than 175 million tons per year, but a more precise figure is unknown without further analysis of volumetric changes in floodplain storage. However, by 1980, when the main period of sediment sequestration was declining, the total amount of sediment stored within the floodplain behind groynes and levees as a result of engineering projects dating back to the early part of the twentieth century was approxi- mately 3.2 gigatons. This volume implies an average accumulation rate of about 45 million tons per year, averaged throughout the 1910-1981 period, or more representatively a rate of about 100 Mt/yr averaged throughout 1930-1960, the period of most intensive engineering activity. On the basis of samples excavated from trenches on the floodplain, the grain-size com- position of this stored sediment has been estimated to be 78 percent sand and 22 percent silt-clay (Jacobson et al., 2009). Given that Lewis and Clark Lake behind Gavins Point Dam captures all free sediment from upstream dams, the post-impoundment Missouri carries essentially no load (0.25 Mt/yr) at Yankton, South Dakota, and then begins to recruit sediment from its bed and tributaries so that the load increases to 7.3 Mt/yr by Sioux City, Iowa, and 58 Mt/yr (~25 percent sand) at Hermann, Missouri. Recruitment of sediment from the bed has resulted in degradation of the average bed elevation by about 10 feet at Yankton, di- minishing downstream to approximately zero in the Omaha-Nebraska City reach. Despite additions of sediment from the tributaries, the bed elevation is reduced also by about 2 to 8 feet due to commercial sand dredging in the vicinity of Kansas City. Loads generally have decreased since dam closure, or at least since the 1993 flood, especially beyond Nebraska City down- stream of the Platte confluence. Reasons for this decline are probably some combination of gradual stabilization of the degraded channel, intensified flushing of the sediment from the river by the 1993 flood, commercial sand dredging, and especially reduction of sediment eroded from the tributary watersheds as a result of land management (dredged sand amounts to ap- proximately 40 percent of the sand load at Hermann).

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41 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES CHANGES TO MISSOURI RIVER ECOLOGY Effects on Missouri River Fishes Changes in Missouri River hydrology, and the dynamics and volumes of sediment transport, during the twentieth century have had far-reaching ef- fects on river ecology and its assemblage of biota. The Missouri River’s na- tive fish species evolved in environments with high turbidity, swift current, a scarcity of quiet backwaters, and an unstable sand-silt bottom (Pflieger, 1971)—habitat conditions that were altered and diminished substantially during the twentieth century. As a result of marked habitat changes, there have been many effects on the river’s native fishes. The term “big river” fish was coined to describe the distinctive assem- blage of fishes in the Missouri and lower Mississippi river system (Pflieger, 1971). Within the Missouri River, species that are predominately benthic specialists reside and exhibit a diversity of ecomorphological adaptations for high turbidity (Galat et al., 2005). These adaptations include reduced eyes, external taste buds and olfactory receptors on dorsal and pectoral fins, and an array of well-developed electrosensory organs and chemosensory organs to navigate, locate food, and avoid predation in a low-visibility environment. The environmental factors that influenced the anatomy of Missouri River’s fishes are similar to those operating in other largely tur- bid, dryland rivers like the Colorado (Mueller, 2005) and the Rio Grande (Calamusso et al., 2005). As sediment concentrations have declined in the Missouri, there has been a corresponding decline of fishes that historically occupied highly turbid main-channel habitats and their replacement by visually feeding species that are competitively superior in less turbid waters (Bonner and Wilde, 2002; Cross and Moss, 1987; Pflieger and Grace, 1987). Decreases in specialized native big river fishes have been attributed to reductions in suspended sediment and turbidity in the lower Missouri River, includ- ing the now federally listed as endangered pallid sturgeon, and imperiled paddlefish, blue sucker, and flathead chub (Pflieger and Grace, 1987). More recently, 11 of the Missouri’s 73 big river fishes were identified by two or more mainstem states as imperiled due to a combination of factors includ- ing impoundment, changes in flow and temperature regimes, reductions in channel habitat complexity, reduced turbidity, and introduced fishes (Galat et al., 2005). Corresponding increases in abundance have occurred in sight-feeding carnivorous fishes that feed on open-water zooplankton in clear water. In many reaches of the river today, non-native sport fishes are in greater abundance than native species. These non-native species often are more tolerant of altered conditions of temperature, turbidity, and habitat (NRC, 2002).

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42 MiSSOuRi RivER PlANNiNg Much of the attention on Missouri River native fish species today re- volves around one species: the pallid sturgeon (Scaphirhynchus albus). The pallid sturgeon was listed as endangered throughout its entire range in Sep- tember 1990. Some scientists consider the species as being close to extinc- tion (Dryer and Sandvol, 1993). Pallid sturgeon inhabited and utilized the floodplains, backwaters, sloughs, and main channel pools and snags in the preregulation Missouri River. Some scientists have expressed concern that the pallid sturgeon cannot reproduce in the Missouri River’s postregulation channelized and reservoir habitats (Henry and Ruelle, 1992; Ruelle and Henry, 1994). The Corps of Engineers and the U.S. Fish and Wildlife Ser- vice today are implementing actions along the Missouri River, downstream of Gavins Point Dam in South Dakota, Nebraska, Iowa, and Missouri, designed to improve habitat conditions for the pallid sturgeon (Chapter 4 provides details on the Corps’ ongoing Missouri River emergent sandbar habitat and shallow water habitat projects). These actions are being taken in accord with a 2000 federal Biological Opinion, and amended in 2003, to avoid jeopardizing the continued existence of the pallid sturgeon. (Chapter 3 provides details of the Fish and Wildlife Service Biological Opinion.) Effects on Missouri River Birds Hundreds of native species of birds use the Missouri River ecosystem for nesting. Many of them occupy the successionally diverse forests on the floodplain and riverine islands. Two bird species, the least tern (Sterna antil- larum) and the piping plover (Charadrius melodus), are federally listed as endangered and threatened, respectively. Both these birds nest in shallow, inconspicuous depressions in sandy or gravelly patches on sandbars with little or no vegetation. Least tern adults are aerial foragers that hover over shallow water in nearby river channels and floodplain habitats and dive after small fishes to feed their young. In contrast, piping plover chicks are precocious and both adults and young forage on the ground primarily along sparsely vegetated sandbar perimeters. Spring floods of the preregulation Missouri River provided an annual, replenished supply of emergent sandbar habitat for tern and plover nesting. The high river stages reached during floods left correspondingly high sand- bars available for nesting after flood cessation that were safe from being overtopped and destroyed by summer rainstorm pulse flows. Impoundment of the Missouri River behind mainstem dams sharply reduced upstream sources of sediment needed to create and maintain sandbars for tern and plover nesting. These poor nesting conditions resulted in loss of critical nesting and chick-rearing habitat and contributed to the listing of the inte- rior least tern by the U.S. Fish and Wildlife Service in 1985 as endangered and the Great Plains population of the piping plover in 1986 as threatened.

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43 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES The few sandbars remaining in the postdevelopment river are topo- graphically low because of low spring river stages. This produces an eco- logical trap for these birds, as sandbars attractive for nesting early in the breeding season are vulnerable to being scoured by high flows. Today, the Corps of Engineers releases small pulses (rises) from Gavins Point Dam dur- ing the prenesting season for terns and plovers to encourage them to nest at the highest elevations on remnant and constructed sandbars below Lewis and Clark Lake. Tributary (e.g., James River) or mainstem flow pulses have helped reduce nesting mortality during the nesting season. Effects on Riparian Floodplain Vegetation The preregulation Missouri River ecosystem was a storehouse of bio- logical diversity maintained by a highly dynamic flow and sediment regime. The active river channel moving across its broad floodplain created enor- mous environmental heterogeneity and a complex mosaic of aquatic, ripar- ian, and terrestrial ecosystems, including in-channel islands and sandbars, oxbow lakes, marshes, sand dunes, and riparian forests (see also Figure 2-4). The riparian forests were dominated by cottonwood, a pioneer spe- cies whose regeneration is dependent on the creation of sandbars during floods (and by the bar building process illustrated in Figure 2-4). Continual reworking and reforming of sandbars associated with the river channel con- tinually created unvegetated and high sandbars for the successful nesting of least terns, piping plovers, and other riverine bird species. Expansive ripar- ian forests on the upper Missouri River floodplain formed a successional se- ries, with a wide age range from young cottonwood–willow forests a decade or two old occupying low benches, to later successional forests dominated by green ash, box elder, and American elm on high benches old enough to have lost all traces of the cottonwood pioneer element. Cottonwood does not regenerate successfully in its own forests. Maintenance of a wide age range of forests, and hence high biological diversity, was dependent on river channel meandering and periodic widening during floods. The Missouri River’s riparian forests were greatly altered by coloniz- ing Europeans, beginning with heavy cutting for steamboat fuel during the mid-nineteenth century, clearing for agriculture, and most recently by channelization and alteration of the river’s flow and sediment regime after construction of the large dams and reservoirs (NRC, 2002). A comprehen- sive survey on the upper Missouri found a surprisingly rich assemblage of 220 vascular plant species growing in the floodplain forests, long after the construction of the large dams and clearing of half or more of the floodplain forest (Johnson et al., 1976; Keammerer et al., 1975). Changes in the river’s hydrologic and sediment regimes caused by the BSNP and Pick-Sloan projects have important implications for trends in

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44 MiSSOuRi RivER PlANNiNg river and floodplain ecosystems. For example, the cottonwood forests that remain as a legacy of the preregulation Missouri River cannot be sustained by the present low rates of river meandering and widening (Johnson, 1998; Johnson and Nelson-Stastny, 2006). Downstream of the large dams, how- ever, floods still occur where levees have been removed or damaged, and cottonwoods have regenerated on flooded farm lands. In-channel nesting birds face similar prospects because of the absence of floods that historically created sandbar islands in the river that are required for their successful nesting. DATA FOR EVALUATING MISSOURI RIVER SEDIMENT DYNAMICS A systemwide understanding of the sources, traps, and modes of transport of sediment through the Missouri River system is important for well-informed sediment-related decisions, including but not limited to en- dangered species protection. The Missouri River basin historically was the focus of extensive data collection and research, and today’s river managers and scientists are heirs to a remarkable legacy of prior investigations. Over time, however, as experts retired and funding diminished, the institutional memory that developed and participated directly in these programs has faded. Moreover, even though the legacy of these Missouri River sediment studies and data collection efforts is extensive and rich, there have been few efforts devoted to periodically organizing, updating, and systematically archiving this large body of information. Given the recent establishment of multiple and significant sediment-related initiatives for the river system, such as the Missouri River Ecosystem Recovery Plan (MRERP and as dis- cussed in Chapter 3), there is a clear need for a systemwide framework for better quantifying sedimentary processes. Extensive historical data were collected by the Corps of Engineers’ Missouri River Division offices in Omaha (the Omaha district office today is part of the Corps’ Northwestern Division) and Kansas City. Much in- formation on Missouri River sediment today exists in archives and earlier reports produced or sponsored by the (former) Missouri River Division of the Corps of Engineers. Today, the Corps of Engineers is the primary funding agency for the collection of sediment data in the river, but actual measurements are made by USGS investigators, working with Corps per- sonnel. The USGS today maintains several offices along the Missouri River including Kansas City (Lee’s Summit, Missouri); Columbia, Missouri; and Council Bluffs, Iowa. Important new observations and syntheses are be- ing developed (e.g., Blevins, 2006; Jacobson et al., 2007, 2009; Jacobson and Galat, 2008). Many current efforts toward improved knowledge of the river’s sedimentary processes are being carried out via cooperation be-

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45 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES tween USGS and Corps of Engineers scientists (e.g., Jacobson et al., 2009). Notwithstanding the vast amount of sediment-related data and analyses, including these ongoing cooperative efforts between the USGS and the Corps of Engineers, there is no single, centralized, sediment database for the Missouri River. The lack of a centralized, accessible sediment database may be inhibit- ing better understanding of sediment dynamics of the Missouri River sys- tem. Moreover, given plans for future system-wide ecosystem management (see the discussion of the Missouri River Ecosystem Restoration Plan in Chapter 3), there will be a need for a centralized database and sediment budget as a foundation for planning, designing, and monitoring the results of various sediment management activities (see Box 2-1 for discussion of centralized data systems in the Florida Everglades and Colorado River). An important step toward a more systematic understanding of the river’s sediment dynamics would be to create a sediment budget for the entire Missouri River, from its headwaters to its mouth. The general frame- work for such a budget is presented in Figure 2-9. Sediment-related data for the Missouri River today are available as maps, aerial photographs and other remotely sensed imagery, hydrologic and sediment measurements, and model-based results. Creation of a centralized data management system may open new perspectives and possibilities for research and management. Such a system of course will not be created immediately; construction of a river-wide sediment budget would be useful first step. The data in Figure 2-9 are from published reports or public presenta- tions provided by the Corps of Engineers and the USGS. In many cases, and despite productive, useful ongoing Corps–USGS collaboration, data are still being processed and a complete summary reference is not yet avail- able. These circumstances illustrate the need for a consistent and clearly documented database for Missouri River basin sediment. In Figure 2-9, the boxes represent sediment flux in volumes of material per year (with input data mainly from Jacobson et al., 2009). In the course of constructing this diagram, it became clear that there are gaps regarding the archiving and organization of those data. For example, sediment data for the Missouri River exist in multiple formats (e.g., paper documents, electronic data files) and are physically located in many differ- ent offices across the basin. There are no directories listing where the data sources reside or how they might be accessed. Furthermore, the values in Figure 2-9 are products of calculations and estimates from heterogenous sources with unknown reliability. Sediment fluxes into reservoirs, for ex- ample, are based on reservoir surveys that measure some combination of coarse bed load and fine suspended load deposited into that reservoir; other boxes are based only on measurements of suspended-sediment flux. The mixing and combining of these data can lead to confusion and may blur

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46 MiSSOuRi RivER PlANNiNg BOX 2-1 Data Collection and Ecosystem Management in Large U.S. River Systems Federal and state scientists working in other large U.S. river systems have faced similar data collection challenges that are encountered today in the Missouri River basin. Experiences from other U.S. river and aquatic systems thus may provide useful information and lessons for the Corps of Engineers, the U.S. Geological Sur- vey, other federal agencies, and state-level managers and scientists. In particular, science and data collection programs in the Florida Everglades and the Colorado River through the Grand Canyon—and the interagency cooperation in both river systems—may be useful in informing future similar efforts for the Missouri River. In the case of the Everglades, the Comprehensive Everglades Restoration Plan (CERP) is being executed by the Corps of Engineers and its partner state agency, the South Florida Water Management District. As in the Missouri River, restoration of the “River of Grass” in the Everglades entails huge amounts of historical data with extensive modern measurements covering a broad region. The Everglades restoration program uses a data management system that is largely under the control of the U.S. Geological Survey. The data are available in a Web-based system, the South Florida Information Access system (http:// sflwww.er.usgs.gov/), which facilitates sharing of available data, ranging from his- torical data to up-to-date monitoring data from field collections. The data include measurements, documentary data, historical reports and aerial photography, and information developed from measurements. Scientists, managers, and decision makers have ready access through internet portals to all the data, as does the general public. Stakeholder groups may not always agree on policies or decisions the Everglades restoration process, but they often agree on the basic data. The data generally provide an agreeable starting point for debate, which is lacking along the Missouri River. Data management systems for the Colorado River in the Grand Canyon pro- vide a second instructive example. The U.S. Department of the Interior conducts ecosystem monitoring along the river in Grand Canyon National Park as part of efforts to evaluate and mitigate downstream impacts of the operations of the Glen Canyon Dam. The setting is similar to the Missouri River in that one agency—the U.S. Bureau of Reclamation—is responsible for large dam operations, while another agency—the U.S. Geological Survey—is responsible for downstream ecosystem data collection. Although the data collection and evaluation program for the Grand Canyon was slow to start, and exhibited some of the same problems of diffuse and disparate data (on sediment as well as other ecological variables) that exist today in the Missouri River case, the Bureau of Reclamation made substantial efforts to centralize its data management at the behest of a National Research Council review (NRC, 1987). The effort was so successful that the U.S. Geological Survey developed a special facility for the purpose: the Grand Canyon Monitoring and Re- search Center (GCMRC) in Flagstaff, Arizona. The GCMRC employs full-time data management personnel within its Information Office, which houses a geographic information system, remotely sensed data, and all data collected by the GCMRC science programs. One Colorado River program especially relevant to the Missouri River is an Integrated Quality of Water Program (IQWP), which includes data collec- tion for sediment mass-balance transport calculations for the canyon.

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FIGURE 2-9 A generalized framework for a Missouri River sediment budget. 47 SOURCE: Data from Boyd et al., 2009; Hotchkiss and Huang, 1994; Jacobson et al., 2009; Stark and Pridal, 2009, USACE, 1996. Figure 2-9.eps landscape bitmap

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48 MiSSOuRi RivER PlANNiNg important distinctions regarding differences in sediment sizes. Especially lacking are systematic measurements that distinguish fluxes of coarse bed- material load from finer washload. Detailed understanding of the respective fluxes of coarse sediments and finer sediments is fundamental information for river system managers attempting to create habitat mitigation and restoration projects both on the Missouri River and downstream as far as coastal Louisiana. An explicit and clearly defined sediment budget for the Missouri River would, for example, help inform current debates regarding the significance of sediments deposited from Corps of Engineers habitat creation programs (discussed in further detail in Chapter 4) to the overall nutrient and sediment flux from the Missouri to the Mississippi River. SUMMARY Prior to channelization, bank stabilization, and the construction of mainstem dams and reservoirs, the Missouri River transported huge amounts of sediment derived from diverse watersheds throughout its drain- age basin. Key source regions of sediment included clay-rich soils developed on the shale beds in the Dakotas, wind-deposited silty loess in northwestern Iowa and eastern Nebraska, the Sand Hills of central Nebraska drained by the Niobrara and Platte rivers, and other sources in the lower Missouri River basin. This sediment provided the building material for the river’s physical structure of channels, islands, bars, and floodplains. The preregulation Mis- souri River’s large sediment load and high turbidity were important to the survival and propagation of native plants, fish, and bird species. Sediment delivered to the Mississippi River was significant in building and sustaining coastal wetlands. The preregulation Missouri River carried a natural load of chemicals and nutrients, some of which were dissolved, some of which were attached to sediment. Of special relevance to the context of today’s key Missouri River management decisions is that the river transported a natural level of phosphorus—a nutrient of broad interest today because of its role in hypoxia in the northern Gulf of Mexico. Excess sediment can be a major problem in some instances, such as in clear-water tributaries with low levels of naturally occurring sediment and with species that evolved in less turbid environments. Question 1 in this report’s statement of task asks, “How and why is sediment a significant variable in the environmental restoration of a river system like the Missouri River?” • Most of the historical, preregulation Missouri River was a sedi- ment-rich system. However, not all tributaries of the Missouri River were sediment rich;

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49 CHANgES iN MiSSOuRi RivER SEDiMENT AND RElATED PROCESSES • For many river processes and services, sediment concentrations and transport are as important as the quantity and flow of water. For example, sediment is the basic building material for river landforms that, among other things, support habitats for native riverine flora and fauna; • High concentrations of sediment and high turbidity in the pre- regulation river were important to the evolution and adaptation of native species such as the pallid sturgeon; • Sediment delivered from the Missouri River to the Mississippi River was historically significant in sustaining coastal wetlands in the ac- tively accumulating lobes of the Louisiana delta. The Missouri River system was transformed in fundamental ways during the twentieth century. The BSNP and the Pick-Sloan Plan dams and reservoirs were implemented to gain a greater degree of control over the river’s hydrologic and geomorphic processes. The purposes of these structures included the goals of flood control, hydropower generation, water supply, and commercial navigation, all with far-reaching social and economic benefits. In altering the river’s hydrologic and sedimentary re- gimes, these projects had major effects on the ecological structure of the river landscape, its vegetation communities, and the habitats for the river system’s native fish and bird species. The dams and reservoirs reduced peak flood discharges, thus reducing the river’s ability to erode and transport sediment downstream. The mainstem dams and reservoirs trapped large amounts of sediments that previously moved through the system and into the Mississippi River and its delta. In addition, vast amounts of sediment that previously moved episodically through the river system have been im- mobilized behind revetments and river-training structures along the river downstream of Gavins Point Dam. The reduced volumes of sediment transported by the postregulation Missouri River directly relate to one question in this report’s statement of task. Question 5 in that statement asks, “Are there long-term consequences to the lack of sediment in the system to the human environment, either economically or environmentally?” The answer may be summarized as • reduced turbidity; • loss of habitat for some native species; • bed degradation downstream of dams and extensively along the main channel and the lower reaches of tributaries. This causes problems for infrastructure by undermining levees and bridge foundations and lowering water levels at municipal water intakes; and • reduced volumes of sediments transported downstream to the Mis- sissippi River and delivered to the Mississippi River delta region.

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50 MiSSOuRi RivER PlANNiNg The Missouri River basin once was a site of major sediment research. Over time, however, priorities shifted, expertise on Missouri River sediment has dwindled, and there has been a decline in the attention paid to overall data collection, management, analysis, archiving, and access. Historical Missouri River sediment data are extensive, and there are important studies of sediment dynamics being conducted today in the basin, including ongo- ing collaborative efforts between Corps of Engineers and USGS scientists. In general, however, sediment-related data and studies are diffuse and scat- tered across the basin in a variety of locations and a variety of formats. A more systematic platform of sediment measurements, data archiving, and systemwide modeling knowledge will be necessary to support efficient deci- sion making for ecosystem management initiatives. The systems and processes for evaluating, archiving, and retrieving Missouri River sediment are fragmented and not well organized. These gaps are of special concern given plans for future investments in Missouri River ecosystem management and reevaluation of authorized purposes for the Missouri River mainstem dams and the Bank Stabilization and Naviga- tion Project. Effective project implementation, operations, and management requires useable knowledge of sediment dynamics; this includes quantities and fluxes of suspended and coarse bedloads, and changes in sediment storage and resultant changes in channel morphology. More informed fu- ture Missouri River resource management decisions would benefit from a comprehensive and accessible Missouri River sediment database and sedi- ment budget. Corps of Engineers and USGS scientists have been conducting valuable collaborative investigations of Missouri River sedimentary processes that should be used as the foundations for a more detailed and extensive sedi- ment budget. Over time, continued collaboration may lead to a more for- mal program for data collection and evaluation. The Corps and the USGS should extend their collaborative efforts and develop a detailed Missouri River sediment budget from the headwaters to the river’s mouth, with pro- visions for continuing revisions and updates as new data become available.