W a t e r

invertebrate

Macro- s

Vegetation

Status and Trends of Selected Resources 

of the Upper Mississippi River System

Long Term Resource Monitoring Program

Status and Trends of Selected Resources 

of the Upper Mississippi River System 

A Synthesis Report of the 

Long Term Resource Monitoring Program

Edited by

Barry L. Johnson and Karen H. Hagerty

 U.S. Geological Survey 

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road 

La Crosse, Wisconsin 54603

December 2008
ii

Suggested citation:

Johnson, B. L., and K. H. Hagerty, editors. 2008. Status and trends of selected resources of the Upper 

Mississippi River System. U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La 

Crosse, Wisconsin, December 2008. Technical Report LTRMP 2008-T002. 102 pp + Appendixes A–B. 

Additional copies of this report may be obtained from the National Technical Information Service, 5285 

Port Royal Road, Springfi eld, VA 22161 (1-800-553-6847 or 703-487-4650). Also available to registered 

users from the Defense Technical Information Center, Attn: Help Desk, 8725 Kingman Road, Suite 0944, Fort 

Belvoir, VA 22060-6218 (1-800-225-3842 or 703-767-9050).
iii

Contents

Page

Acknowledgments ................................................................................................................................................vi

Executive Summary .............................................................................................................................................. 3

Chapter 1. Introduction ....................................................................................................................................... 11

1.1 The Upper Mississippi River System ................................................................................................... 11

1.2 Purpose and Scope of the Status and Trends Report ............................................................................ 11

1.3 The Ecosystem of the Upper Mississippi River System ...................................................................... 11

1.3.1 Historical Conditions .................................................................................................................. 12

1.3.2 Existing Conditions ................................................................................................................... 15

1.4 Monitoring and Managing the River: The Environmental Management Program .............................. 16

1.5 Desired Future Conditions: Providing the Foundation for Developing Objectives ............................. 17

1.6 Ecological Drivers, Stressors, and Indicators ....................................................................................... 17

1.6.1 Indicator Development ............................................................................................................... 18

1.6.2 Linking Ecosystem Goals, Objectives, and Indicators ............................................................... 19

Chapter 2. Status and Trends of Resources in the Upper Mississippi River System .......................................... 23

2.1 Introduction .......................................................................................................................................... 23

2.2 River Hydrology Indicators .................................................................................................................. 24

2.2.1 Mean Annual Discharge ............................................................................................................. 24

2.2.2 Seasonal Cycle of Water Elevation ............................................................................................. 27

2.3 Water Quality Indicators ....................................................................................................................... 30

2.3.1 Major Nutrients (Total Nitrogen and Total Phosphorus) ............................................................ 30

2.3.2 Chlorophyll a .............................................................................................................................. 31

2.3.3 Total Suspended Solids ............................................................................................................... 34

2.3.4 Dissolved Oxygen ...................................................................................................................... 36

2.3.5 Suitable Winter Habitat for Sunfi shes in Backwaters ................................................................ 40

2.4 Sedimentation Indicators ...................................................................................................................... 43

2.4.1 Depth Diversity in Upper Impounded Areas .............................................................................. 43

2.4.2 Net Sedimentation Rates in Backwaters of the Upper Impounded Reach ................................. 45

2.5 Land Cover/Land Use Indicators .......................................................................................................... 48

2.5.1. Floodplain Forest ........................................................................................................................ 48

2.5.2. Emergent Vegetation ................................................................................................................... 50

2.5.3. Area of Floodplain Behind Levees ............................................................................................. 52

2.6 Aquatic Vegetation Indicators .............................................................................................................. 55

2.6.1. Submersed Aquatic Vegetation ................................................................................................... 55

2.7 Macroinvertebrate Indicators ................................................................................................................ 58

2.7.1. Burrowing Mayfl ies .................................................................................................................... 58

2.7.2. Fingernail Clams ........................................................................................................................ 60

2.8 Fish Indicators ...................................................................................................................................... 63

2.8.1. Bluegill ....................................................................................................................................... 63

2.8.2. Channel Catfi sh .......................................................................................................................... 65

2.8.3. Sauger ......................................................................................................................................... 67

2.8.4. Smallmouth Buffalo ................................................................................................................... 67

2.8.5. Forage Fish Index ....................................................................................................................... 70

2.8.6. Species Richness ...................................................................................................................... 70

2.8.7. Nonnative Fishes ........................................................................................................................ 73

2.8.8. Recreationally Harvested Native Fishes ..................................................................................... 75

2.8.9. Commercially Harvested Native Fishes ..................................................................................... 76

Chapter 3. Discussion, Conclusions, and Recommendations ............................................................................. 81

3.1 Integrity and Sustainability of the Upper Mississippi River System .................................................. 81

3.1.1 Implications for Ecosystem Integrity and Sustainability ........................................................... 81

3.1.2 Comparison of Status and Trends among Regions and Indicators ........................................... 81
iv

Page

3.2 Use and Application of LTRMP Component Data ............................................................................... 87

3.2.1 Condition of the Ecosystem ........................................................................................................ 87

3.2.2 Planning and Decision Making .................................................................................................. 88

3.2.3 Ecosystem Restoration and Management ................................................................................. 89

3.3 Future Efforts ........................................................................................................................................ 89

3.3.1 Enhancing Assessment of Status and Trends ............................................................................. 89

3.3.2 Improving Indicator Selection .................................................................................................... 90

3.3.3 Conclusions ............................................................................................................................... 91

References ........................................................................................................................................................... 93

Appendix A - Glossary ...................................................................................................................................... 103

Appendix B - Acronyms ................................................................................................................................... 107

Tables

Page

Table 1.1. Ecological context of indicators derived from the Long Term Resource Monitoring Program. ... 20

Table 2.1. Gaging stations on the Upper Mississippi River System used for analyses of elevations 

and discharge. ............................................................................................................................................. 24

Table 2.2. Mean proportion of stratifi ed random sampling sites with dissolved oxygen concentration less 

than 5 mg/L in winter and summer from 1993 to 2001. ............................................................................ 38

Table 2.3. Common and scientifi c names of the 19 species that were combined to create an 

index for recreationally harvested fi shes. ................................................................................................... 75

Table 2.4. Common and scientifi c names of the seven native species that were combined to create an 

index for commercially harvested fi shes ..................................................................................................... 76

Figures

Page

Figure 1.1. Map of the basin of the Upper Mississippi River System showing the four major geomorphic 

reaches ......................................................................................................................................................... 13

Figure 1.2. Human stressors on the Upper Mississippi River ecosystem ........................................................ 18

Figure 2.1. Mean annual discharge on the Upper Mississippi River System from 1950 to 2004 ................... 26

Figure 2.2. Average annual hydrographs of water elevation on the Upper Mississippi River System ............ 28

Figure 2.3. Total nitrogen (TN) concentrations in the main channel of the six Long Term Resource 

Monitoring Program study reaches from 1994 to 2002 ............................................................................... 32

Figure 2.4. Total phosphorus (TP) concentrations in the main channel stratum of the six Long Term 

Resource Monitoring Program study reaches from 1994 to 2002 ............................................................... 33

Figure 2.5. Chlorophyll a concentrations in the main channel stratum of the six Long Term Resource 

Monitoring Program study reaches from 1994 to 2002 ............................................................................... 35

Figure 2.6. Total suspended solids concentrations in the main channel stratum of the six Long Term 

Resource Monitoring Program study reaches from 1994 to 2002 ............................................................... 36

Figure 2.7. The percentage of backwater sampling sites where dissolved oxygen concentrations during 

winter, at the surface or just below ice cover, were >5 mg/L (1994–2002) for fi ve study reaches of the 

Long Term Resource Monitoring Program .................................................................................................. 39

Figure 2.8. Percent of backwaters that contained suitable habitat for sunfi shes during winter from 1994 

and 2002 based on a combination of temperature, dissolved oxygen, and depth in study reaches of the 

Long Term Resource Monitoring Program that have backwater habitats. .................................................. 41

Figure 2.9. Mean percentage of backwater with suitable conditions during winter from 1994 and 2002 

for temperature, dissolved oxygen, and depth in study reaches of the Long Term Resource Monitoring 

Program that have backwater habitats. ....................................................................................................... 42
v

Page

Figure 2.10. Change in water depths for the impounded areas in Pools 4, 8, and 13 of the Upper 

Mississippi River from 1940 to 1990 .......................................................................................................... 44

Figure 2.11. Annual net sedimentation rates for aquatic areas and terrestrial areas in backwaters of 

Pools 4, 8, and 13 between 1997 and 2001 .................................................................................................. 46

Figure 2.12. The area of fl oodplain forest in the Upper Mississippi River System based on 1989 and 2000 

land cover maps produced by the Long Term Resource Monitoring Program ............................................ 49

Figure 2.13. The area of emergent vegetation in the Upper Mississippi River System based on 1989 and 

2000 land cover maps produced by the Long Term Resource Monitoring Program ................................... 51

Figure 2.14. The percentage of the total fl oodplain area that was behind levees within the Upper 

Mississippi River System based on levee coverage developed by the Scientifi c Assessment and 

Strategy Team then applied to the 2000 land cover maps produced by the Long Term Resource 

Monitoring Program .................................................................................................................................... 53

Figure 2.15. Percent frequency of occurrence of submersed aquatic vegetation in the Long Term 

Resource Monitoring Program sampling pools from 1991 to 2004 ............................................................ 56

Figure 2.16. Estimated density of mayfl ies weighted by area of strata within each study area of the Long 

Term Resource Monitoring Program from 1993 to 2004 ............................................................................ 59

Figure 2.17. Estimated density of fi ngernail clams weighted by area of strata within each Long Term 

Resource Monitoring Program study area from 1993 to 2004 ................................................................... 61

Figure 2.18. Catch per unit effort of bluegill >150mm total length from 1993 to 2004 in six trend areas 

monitored by the Long Term Resource Monitoring Program using day electrofi shing .............................. 64

Figure 2.19. Catch per unit effort of channel catfi sh >280mm total length from 1993 to 2004 in six trend 

areas monitored by the Long Term Resource Monitoring Program using large hoopnets .......................... 66

Figure 2.20. Catch per unit effort of sauger >200mm total length from 1993 to 2004 in six trend areas 

monitored by the Long Term Resource Monitoring Program using day electrofi shing .............................. 68

Figure 2.21. Catch per unit effort of smallmouth buffalo >280mm) total length from 1993 to 2004 in six 

trend areas monitored by the Long Term Resource Monitoring Program using large hoopnets ................. 69

Figure 2.22. Catch per unit effort of the forage index of emerald shiner and gizzard shad from 1993 

to 2004 in six trend areas monitored by the Long Term Resource Monitoring Program using day 

electrofi shing. ............................................................................................................................................... 71

Figure 2.23. Species richness from 1993 to 2004 in six trend areas monitored by the Long Term 

Resource Monitoring Program .................................................................................................................... 72

Figure 2.24. Percentage of total fi sh biomass accounted for by nonnative species from 1994 to 2002 in 

six trend areas monitored by the Long Term Resource Monitoring Program ............................................. 74

Figure 2.25. Catch per unit effort of recreationally harvested fi shes captured with day electrofi shing from 

1994 to 2004 by the Long Term Resource Monitoring Program ................................................................. 77

Figure 2.26. Catch per unit effort of commercially harvested fi shes captured with day electrofi shing from 

1994 to 2004 by the Long Term Resource Monitoring Program ................................................................. 79

Figure 3.1. Comparison of ratings of the status and trends for resource indicators derived from 

data collected at the six study areas of the Long Term Resource Monitoring Program on the 

Upper Mississippi River System ................................................................................................................. 82

Figure 3.2. Data on density of fi ngernail clams and mayfl ies from the Long Term Resource Monitoring 

Program compared to total number of diving ducks observed in the area of Pool 8 that was closed to 

hunting, 1996–2002 ..................................................................................................................................... 85

Boxes

Page

Box 1.1. Descriptions of the four major fl oodplain reaches composing the Upper Mississippi River 

System .......................................................................................................................................................... 14

Box 1.2. Conceptual Defi nitions of Drivers, Stressors, and Indicators ........................................................... 19
vi

Acknowledgments

The report benefi ted greatly from review Natural Resources, Minnesota Department of 

by many anonymous reviewers from the U.S. Natural Resources, Missouri Department of 

Army Corps of Engineers, U.S. Fish and Wildlife Conservation, and Wisconsin Department of 

Service, U.S. Environmental Protection Agency, Natural Resources. Statistical help was provided 

Illinois Department of Natural Resources, Illinois by Brian Gray, Upper Midwest Environmental 

Natural History Survey, Iowa Department of Sciences Center.
Status and Trends of Selected Resources 

of the Upper Mississippi River System 

A Synthesis Report of the 

Long Term Resource Monitoring Program

Edited by

Barry L. Johnson 

U.S. Geological Survey, Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road, La Crosse, Wisconsin 54603

and 

Karen H. Hagerty

U.S. Army Corps of Engineers, Rock Island District

Clock Tower Building, P.O. Box 2004, Rock Island, Illinois 61204

Section Authors

Robert F. Gaugush, Jeffrey N. Houser, Brian S. Ickes, Kirk Lohman, John C. Nelson, 

Larry R. Robinson, James T. Rogala, Jennifer S. Sauer, and Yao Yin

U.S. Geological Survey, Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road, La Crosse, Wisconsin 54603

Sandra K. Brewer

U.S. Army Corps of Engineers, Rock Island District

Clock Tower Building, P.O. Box 2004, Rock Island, Illinois 61204

J. Therese Dukerschein and James R. Fischer

Wisconsin Department of Natural Resources, Onalaska Field Station

2630 Fanta Reed Road, La Crosse, Wisconsin 54603

and

John H. Chick

Great Rivers Field Station, Illinois Natural History Survey

8450 Montclair Avenue, Brighton, Illinois 62012

U.S. Geological Survey 

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road 

La Crosse, Wisconsin 54603

December 2008

3

Executive Summary

The Upper Mississippi River System

Like other large rivers, the Upper Mississippi River System (UMRS) serves a diversity of roles. 

The UMRS provides commercial and recreational fi shing, fl oodplain agriculture, drinking water for 

many communities, an important bird migration pathway, a variety of recreational activities, and a 

navigation system that transports much of the country’s agricultural exports. These multiple roles 

present signifi cant management challenges. 

Regular assessment of the condition of the river is needed to improve the design of 

conservation and management plans and evaluate their effectiveness. This report provides a 

summary of the recent status (mean and range of conditions) and trends (change in a consistent 

direction over time) for selected indicators of the ecological condition of the Upper Mississippi and 

Illinois Rivers. Data collected by the Long Term Resource Monitoring Program (LTRMP) are used 

to describe biological, physical, and chemical indicators of river condition over 9–12 years in most 

instances. 

The UMRS, as defi ned by Congress in the Water Resources Development Act of 1986, includes 

the Upper Mississippi River from Minneapolis, Minnesota, to Cairo, Illinois (854 river miles); 

the Illinois Waterway from Chicago to Grafton, Illinois (327 miles); and navigable tributaries 

(76 miles). The system consists of the fl oodplain and all associated aquatic and terrestrial habitats, 

which covers approximately 2.6 million acres and includes 10 National Wildlife Refuges. The 

UMRS can be divided into four major reaches based on physical and ecological conditions: (1) the 

Upper Impounded Reach (Pools 1–13), (2) the Lower Impounded Reach (Pools 14–26), (3) the 

Unimpounded Reach (below Pool 26), and (4) the Illinois Waterway.

Historical and Existing Conditions

The UMRS has been modifi ed extensively since the mid-1800s. Modifi cations for navigation 

included removal of fallen trees, use of channel training structures (wing dikes, closing dams) to 

force water into the main channel, dredging, and a series of 37 locks and dams constructed above 

St. Louis in the 1930s. Also, extensive levees were constructed, mainly south of Rock Island, 

Illinois, on the Mississippi River, and Peoria, Illinois, on the Illinois River, to provide fl ood 

protection for urban areas and fl oodplain agriculture. In 1900, the Illinois River was connected 

to Lake Michigan by the Des Plaines River to divert the discharge of Chicago’s sewage to the 

Illinois River. This change increased nutrient inputs to the UMRS and allows exchange of species, 

including invasive species, between the UMRS and the Great Lakes.

The UMRS drainage basin has also been substantially altered by intensive forestry, draining 

of wetlands, and farming, which increased soil erosion, runoff, and sediment input to the UMRS. 

Increasing urbanization and industrialization combined with inadequate wastewater treatment 

resulted in substantial water pollution affecting both human health and river biota. River water 

quality has improved because of better environmental regulation since the 1970s.

The current condition of the UMRS is heavily infl uenced by its agriculture-dominated basin 

and by the dams, channel training structures, dredging, and levees that regulate fl ow distribution 

during most of the year. Although substantial improvements in some conditions have occurred since 

the 1960s because of improvements in sewage treatment and land use practices, the UMRS still 

faces substantial challenges including

1. High sedimentation rates in some backwaters and side channels;

2. An altered hydrologic regime resulting from modifi cations of river channels, the 

fl oodplain, and land use within the basin, and from dams and their operation;

3. Loss of connection between the fl oodplain and the river, particularly in the southern 

reaches of the UMRS; 

4. Nonnative species (e.g., common carp [Cyprinus carpio], Asian carps [Hypophtalmichthys 

spp.], zebra mussels [Dreissena polymorpha]); 

5. High levels of nutrients and suspended sediments; and

6. Degradation of fl oodplain forests.
4

Monitoring and Managing the River: The Environmental Management Program

The Environmental Management Program (EMP) was established by the Water Resources 

Development Act of 1986. The EMP is managed by the U.S. Army Corps of Engineers (USACE) 

and implemented in cooperation with the U.S. Geological Survey (USGS), U.S. Fish and 

Wildlife Service, U.S. Environmental Protection Agency, U.S. Department of Agriculture Natural 

Resources Conservation Service, and the fi ve UMRS states (Illinois, Iowa, Minnesota, Missouri, 

and Wisconsin). The EMP consists of two principal components. The Habitat Rehabilitation 

and Enhancement component works to rehabilitate the system through implementing projects to 

improve habitats or modify river management practices. 

The other component of EMP is LTRMP. The LTRMP is a multipurpose program of 

monitoring, applied research, and management evaluation designed to achieve the following broad 

goals (U.S. Geological Survey 1997):

1. Develop a better understanding of the ecology of the UMRS and its resource problems,

2. Monitor resource change,

3. Develop alternatives to better manage the UMRS, and

4. Provide for the proper management of monitoring information.

The LTRMP is implemented by the USGS Upper Midwest Environmental Sciences Center 

(UMESC) and six fi eld stations (Figure 1.1; Lake City, Minnesota, Pool 4; La Crosse, Wisconsin, 

Pool 8; Bellevue, Iowa, Pool 13; Alton, Illinois, Pool 26; Havana, Illinois, La Grange Pool; and 

Cape Girardeau, Missouri, Open River) operated by staff from the UMRS states. The Program 

supports a variety of monitoring, data serving, and research efforts. Monitoring data, results of 

various analyses and focused studies, and management tools and models developed under LTRMP 

are publicly available on the World Wide Web. The data and information generated by the LTRMP 

have been used in designing habitat rehabilitation projects and in developing various ecosystem 

restoration plans, including the Upper Mississippi River and Illinois Waterway Navigation Study 

and the Illinois River Basin Restoration Comprehensive Plan. The monitoring component of 

LTRMP is not designed to evaluate individual projects, but to assess changes over time in response 

to larger scale infl uences such as natural fl uctuations and cycles, multiple rehabilitation projects, or 

modifi cations to the watershed, as these effects become evident at the scale of a pool or river reach. 

The core monitoring effort for LTRMP sampled four primary ecological components (fi sheries, 

water quality, aquatic vegetation, and aquatic macroinvertebrates) from six 30–60 mile river 

sections that embody the wide range of environmental gradients within the UMRS. Within these 

six locations, data were collected with a random sampling design and standardized methods, which 

permit rigorous comparisons between locations and over time. Data on land cover, hydrology, and 

bathymetry were also collected, permitting the development of landscape indicators for comparison 

with biological and chemical indicators.

Ecosystem Goals and Indicators

This report focuses mainly on measuring changes in potential indicators of system health as 

derived from LTRMP data. Ideally, indicators should be derived from management objectives 

that defi ne desired future conditions for the UMRS and identify target levels for those indicators. 

However, no common set of goals and objectives has been formally adopted by UMRS 

stakeholders. Informally, river managers have indicated that the future should be characterized by 

improved habitat quality and diversity, a closer approximation of the predevelopment hydrologic 

regime, and a diverse biotic community composed mainly of native species. River regulation, 

sedimentation, and fl oodplain development are generally considered the primary stressors affecting 

river habitats. Clearly articulating ecosystem goals and objectives for a system as large, diverse, and 

complex as the UMRS is exceedingly diffi cult, yet critically important for assessing management 

options and, ultimately, defi ning success.
5

Status and Trends of Indicators of System Health 

For this report, scientists and partners within LTRMP identifi ed 24 potential ecosystem 

indicators. These indicators were chosen because they relate to many of the primary resource 

problems or outcomes important to managers. The 24 indicators are grouped into seven categories: 

hydrology, sedimentation, water quality, land cover, aquatic vegetation, invertebrates, and fi sh. 

Each indicator is evaluated for status across locations and for trends over time, with estimates 

of uncertainty when possible. If quantitative targets for indicators have been recommended by 

managers or in the literature, we identifi ed them (mainly available for water quality). For most 

indicators, however, internal comparisons are used to identify areas that were “better” or “worse” 

than other parts of the river. In some instances, we try to link indicators to suspected drivers or 

stressors, but the collective knowledge base is currently too incomplete to determine causes for the 

patterns observed in most indicators. This is a fertile area for future analyses and research.

River Hydrology

Dams on the UMRS were built mainly to facilitate commercial navigation. They were not 

designed for fl ood control and have little effect on total discharge (Chen and Simmons 1986; 

Sparks 1995); thus, changes in annual discharge are mainly related to precipitation. The eastern 

United States experienced increased discharge since 1970 (McCabe and Wolock 2002), which was 

evident in all reaches of the UMRS (Figure 2.1). During 1993–2004, when the LTRMP data used 

in this report were collected, fl ows were slightly higher than 1970–1992 in the impounded reaches, 

but were similar on the Illinois River and the Unimpounded Reach. Within this period, discharge 

varied substantially with record or near record fl ow in 1993 and relatively low fl ows in 2000 and 

2003. Thus, most of the indicators presented in this report (those covering 1993–2004) represent 

conditions generally wetter than historically on the UMRS. 

Hydrologic data show that, compared to pre-dam conditions, the impounded reaches had 

higher average water elevations, especially during low fl ow periods (Figure 2.2). This refl ects the 

main purpose of the dams, which was to increase water depth at low discharges. This effect can 

be countered somewhat by changing dam operation to reduce water levels during summer while 

maintaining navigation. In the Open River Reach, the annual cycle of water elevations was similar 

between pre- and post-dam periods (Figure 2.2), but channel shape and hydraulics have been 

substantially altered from historical conditions. Some of the effects of changes in hydraulics can 

be countered by re-engineering channel training structures to recreate diversity in fl ows and depth 

within the main channel and side channels. All reaches have experienced increased short-term 

variation in water levels. In some pools, changing from a mid-pool control point to a dam control 

point for water levels may reduce short term variation. However, much of this problem is related to 

changes in the basin that deliver water to rivers more quickly and is outside of the control of UMRS 

managers. 

Substantial changes in annual discharge are not expected in the near future, but in the long 

term, discharge will be linked mainly to climate. If changes in discharge occur, managers will need 

to develop strategies to either maintain critical ecological processes or adapt to changes in those 

processes in ways that allow the river to continue providing the ecological goods and services 

desired by the public. A combination of analyses of LTRMP data and focused research studies 

should help reveal linkages between discharge and ecological processes. 

Water Quality

Water quality among the four river reaches can be considerably different for some indicators, 

but similar for others. The most striking difference is in the concentration of total suspended 

solids (TSS). In Pool 4, TSS are greater in upper Pool 4 than in lower Pool 4 because of settling 

in Lake Pepin, then increase from about 20 mg/L in lower Pool 4 to 200 mg/L in the Open River 

Reach, and are intermediate in the Illinois River (Figure 2.6). In lower Pool 4 and Pool 8, TSS are 

generally less than the recommended maximum concentration for plant growth (25 mg/L) and show 

a downward trend since 1994 for unknown reasons. Other reaches exceed this maximum in most 
6

years with no trends evident. A downstream increase in TSS is a common feature of rivers but is 

likely exacerbated in the UMRS by runoff from agricultural watersheds, which are more prevalent 

in Illinois and Iowa. Reducing the TSS load coming into the UMRS will be diffi cult but may result 

from increased use of best management practices on the watershed or from restoration of tributary 

deltas in the UMRS fl oodplain to trap sediments before they enter the river. 

The nutrients nitrogen and phosphorous were at relatively high levels throughout the UMRS. 

Nitrogen concentrations increase from about 2 mg/L in the Upper Impounded pools to 3 mg/L 

in the lower reaches (Figure 2.3). Phosphorus increased downstream from about 0.1 mg/L in the 

Upper Impounded pools to 0.25 mg/L in the Open River Reach (Figure 2.4). The Illinois River 

generally had the highest concentrations of both nitrogen (4 mg/L) and phosphorous (0.4 mg/L). 

Mean nitrogen concentrations were more than the suggested upper limit (2.18 mg/L) in the Upper 

Impounded pools about 50% of the time, but in the lower reaches, nearly all the time. Mean 

phosphorus concentrations were more than the suggested upper limit (0.08 mg/L) for nearly all 

reaches and years. We found no trends over time. 

Nitrogen levels can be reduced in the UMRS by storage in plants (e.g., forest trees) or by 

diverting more water into off channel areas and wetlands where natural processes can release the 

nitrogen to the atmosphere. However, increasing these processes within the fl oodplain of the UMRS 

alone will not reduce nitrogen enough to eliminate hypoxia in the Gulf of Mexico. That will almost 

certainly require reducing nutrient inputs to the river through more effective treatment of point 

source inputs and reducing losses of nutrients applied to farm fi elds and lawns. 

High nutrient concentrations can cause excess algal growth. Yet all reaches of the UMRS 

generally had medium levels of chlorophyll (a measure of algal abundance) in the main channel 

(Figure 2.5), indicating that algal growth was typically not excessive. However, algae blooms 

(a locally high abundance of, typically, blue-green algae) do occur in the UMRS, usually during 

periods of low fl ow. Blooms, whose value as food is generally quite low, can reduce light 

penetration, which reduces growth of rooted aquatic plants. More work is needed on the species 

composition and production of the algal community under different combinations of fl ow and 

nutrient loads to determine potential ecological effects. 

Dissolved oxygen levels were generally good throughout the system (Figure 2.7), but with 

occasional episodes of low oxygen (<5 mg/L) in backwaters and in the main channel in La Grange 

Pool of the Illinois River (Table 2.2). Low oxygen in backwaters typically occurs during low fl ow 

periods when backwaters are poorly mixed and zones of high oxygen demand develop. Managers 

have been successful at changing water fl ow patterns to introduce more oxygen rich water into 

critical backwaters and increase oxygen levels. 

Winter habitat conditions can cause stress, or even mortality, for fi sh in rivers. Research 

supported by the LTRMP identifi ed suitable winter conditions for sunfi shes in backwaters as 

dissolved oxygen concentration >5 mg/L, temperature >1.0°C, and water depth >0.33 m. In the 

UMRS, only a small percentage of the total backwater area meet these criteria in the upper pools, 

but percentages are much higher in lower pools (Figure 2.8). However, despite relatively little 

suitable winter habitat, bluegills (Lepomis macrochirus), a typical backwater species, are abundant 

in the upper pools; thus, the usefulness of this metric as an indicator is questionable. Suitable winter 

habitat is relatively rare in many river systems (Cunjak 1996), but suitable areas often support high 

densities of fi sh during winter (Carlson 1992; Raibley et al. 1997). We do not know how much 

suitable winter habitat is needed within a river reach, nor how well fi sh survive in areas that do not 

meet the suitability criteria. More investigation is needed of the effect of winter habitat suitability 

compared to other factors affecting the abundance of sunfi shes.

Sedimentation and Habitat Diversity

In all reaches, sedimentation has fi lled-in many backwaters, channels, and deep holes. In the 

lower reaches, sediments have completely fi lled the area between many wing dikes producing 

a narrower channel and new terrestrial habitat. Erosion has eliminated many islands, especially 

in impounded zones. Although annual rates of sedimentation and erosion were highly variable 

(Figure 2.11), the net effect over 50 years was a substantial loss of habitat diversity (Figure 2.10). 
7

We expect sediment inputs to the system to remain high and expect both fi lling and erosion to 

continue, but at slower rates. Habitat diversity can be increased through constructing islands, 

dredging backwaters, and restoring fl oodplain connections. Actions such as reclaiming a levee 

district may produce quick and substantial changes in habitat diversity, whereas smaller-scale 

projects like dredging and island building will likely require multiple projects to signifi cantly 

change habitat diversity at the pool or reach scale. Managers are designing projects that modify 

river fl ows and hydraulics in ways that directly affect the sedimentation and erosion and can help 

sustain habitat diversity naturally. 

Land Cover and Land Use

Floodplain forests in the UMRS cover only a small portion of the area that they did before 

European settlement (Nelson et al. 1994; Yin et al. 1997). Between 1989 and 2000 forest area 

further declined by 5% (17,000 acres) system wide (Figure 2.12). By reach, there was a 2% increase 

in the Unimpounded Reach, but a 4–9% decrease in other reaches. Early forest losses were mainly 

due to logging for steamboat fuel and lumber and subsequent conversion to agricultural and urban 

uses. Impoundment fl ooded many acres of forest and remaining areas are adjusting to the ecological 

effects of changes in water levels. Maintaining high water elevations at low fl ows has increased the 

ground water elevation and caused a shift to trees that can tolerate wetter conditions, mainly silver 

maple (Acer saccharinum). In addition, short-term variation in water levels and high sedimentation 

rates on the fl oodplain have reduced recruitment of trees in some locations. These stressors are 

likely to continue. Reforestation efforts can have positive effects locally, but large scale effects will 

likely require changes in underlying ecological conditions. 

The amount of fl oodplain area sequestered behind levees shows a distinct gradient from 4% 

sequestered in the Upper Impounded Reach to 60–70% in the Unimpounded Reach and lower 

portions of the Illinois River (Figure 2.14). Most of these levees protect land used for agriculture or 

urban areas, but a few are managed as moist soil units for waterfowl habitat. It is unlikely that many 

new levees will be built in the UMRS, although some expansion is still occurring in urban areas. 

Most existing levees are likely to be maintained for the foreseeable future, but some may revert to 

public ownership (if both funding and willing sellers are available) to be managed for ecological 

benefi ts. However, conversions of leveed areas to public land are expected to occur slowly and large 

changes in this indicator are not expected in the near term. 

Floodplains are an important, natural element of the UMRS, but the amount of fl oodplain 

required to maintain critical ecosystem services, such as waste assimilation, biotic diversity, 

and water supply is unknown. Thus, no specifi c targets exist for the amount of active (unleveed) 

fl oodplain required. Management experiments and focused research are needed to determine 

relations between fl ood frequency and ecological responses. However, any management targets for 

amount of active fl oodplain are likely to differ among river reaches given the economic realities of 

current land ownership patterns. 

Submersed and Emergent Vegetation

Aquatic vegetation can play an important role in river ecosystems in a variety of ways 

including nutrient cycling and hydraulics and can provide both a food source and physical habitat. 

Submersed aquatic vegetation was common in shallow backwaters in the Upper Impounded 

Reach (Figure 2.15), but decreased rapidly below Pool 13 and was seldom detected in Pool 26 

or the Illinois River, except in isolated lakes. Submersed vegetation was common historically in 

all reaches except the Open River Reach, which had little appropriate habitat. In upper Pool 4 

(upstream of Lake Pepin) submersed vegetation has declined steadily since 1991, which may be 

associated with relatively high levels of nutrients and turbidity from urban areas and the Minnesota 

River. Lower Pool 4, Pool 8, and Pool 13 experienced fl uctuations in submersed vegetation, but 

appeared to be highly resilient. In Pool 26 and La Grange Pool, small increases in submersed 

vegetation occasionally occurred following lower water levels, but they did not persist. 

The percentage of total area in emergent vegetation averaged about 5% (range 0–10%) among 

reaches and was greatest in the Upper Impounded Reach (Figure 2.13). Between 1989 and 2000, 
8

coverage decreased by about 5000 acres in the Upper Impounded Reach, but increased in all other 

reaches. Changes were most striking in the Illinois River pools (increase of about 7,500 acres), but 

the areal extent of emergent vegetation was still relatively small at about 3%. Some of this increase 

may represent recovery of emergent vegetation following drought conditions experienced during 

1987–89. 

It appears that low water clarity, consistent inundation of shorelines, and high short-term 

variation in water levels are the primary factors limiting distribution of aquatic vegetation. These 

factors are especially evident below Pool 13 and are expected to continue. Large scale techniques 

such as summer drawdowns and changes in dam operations that reduce short-term water level 

variation can enhance conditions for aquatic vegetation. Locally, building islands can create 

areas that are sheltered from current and wind, which allows suspended sediments to settle out 

thus increasing water clarity and plant growth. These techniques have worked well in the Upper 

Impounded Reach and should be evaluated in lower reaches.

Macroinvertebrates

Abundance of mayfl ies (Hexagenia spp.) and fi ngernail clams (Musculium transversum) 

showed a distribution similar to other biotic indicators with high densities in the upper pools but 

consistently lower densities in Pool 26, La Grange Pool, and the Open River Reach (Figures 2.16, 

2.17). The only signifi cant trend observed was an increase in fi ngernail clam density in Pool 8. 

Historically, macroinvertebrate numbers have been highly variable and both mayfl y and fi ngernail 

clam densities are generally within the ranges reported in past studies on the UMRS. Many factors 

could affect annual abundance on mayfl ies and fi ngernail clams, but the variation seen both in 

LTRMP data and historically indicate that these organisms are resilient and able to rebound if 

conditions are right.

Fish

The LTRMP data indicate that most fi sh species known from the UMRS over the past 100 years 

still occur in the river today, although 39 species collected by the LTRMP were considered rare, 

endangered, or threatened by state or Federal agencies. Species richness (the number of species 

collected annually) was similar among study reaches (Figure 2.23) with means ranging from about 

60 to 70 species. However, there was a general north-south dichotomy in UMRS fi sh communities 

refl ecting habitat differences. A northern fi sh community, dominated by fi sh associated with 

backwater and lake-like habitats (e.g., bluegills, largemouth bass [Micropterus salmoides], various 

minnows and shiners) differs from the southern fi sh community that is more associated with main 

channel and side channel habitats (e.g., gizzard shad [Dorosoma cepedianum], buffalo [Ictiobus

spp.], white bass [Morone chrysops]). 

For individual fi sh species, some signifi cant trends were identifi ed. For example, smallmouth 

buffalo (Ictiobus bubalus) increased in all study areas except Pools 8 and 13 (Figure 2.21), channel 

catfi sh increased in Pool 4 and La Grange Pool (Figure 2.19), and bluegills increased in Pools 4 

and 8 (Figure 2.18). A composite indicator for native sport fi shes increased in Pool 4, but decreased 

in La Grange Pool and the Open River Reach (Figure 2.25). The reasons for these changes in a 

single species or assemblage are diffi cult to determine, but in Pool 8, two specifi c management 

actions (island construction and summer water level drawdowns) were implemented to improve 

backwater habitat and may be at least partially responsible for increases in bluegill abundance. 

However, bluegills also increased in Pool 4; thus, the changes in Pool 8 may be due to larger scale 

factors. Additional island building is planned for Pool 8 in the next few years. Continued data 

collection by the LTRMP and specifi c analyses within Pool 8 will increase our ability to identify the 

large-scale effects of rehabilitation projects as more islands are built. 

Nonnative fi shes composed a high percentage of total fi sh biomass (about 30–60%, 

Figure 2.24) in all locations. A high percentage of nonnative fi shes in the community is generally 

considered an ecological impairment, although no specifi c targets have been identifi ed for this 

indicator in the UMRS. Most of the nonnative biomass is from common carp, but recently the 

numbers and biomass of invading Asian carps have increased substantially. A positive note is that 
9

Pools 4, 8, and 13 showed signifi cant decreases in percentage of nonnative biomass over time. 

Further analyses of LTRMP data may reveal factors that correlate with nonnative biomass and 

suggest management strategies to reduce their abundance. Monitoring data alone, however, cannot 

confi rm cause-and-effect relations. Field experiments will be needed to evaluate the effectiveness of 

proposed techniques to reduce nonnative biomass. 

Overall Condition

Taken together, these indicators document ecological impairments in all parts of the system, 

but show a gradient of river health ranging from a relatively healthy system in the northern reaches, 

to one that is much less healthy in the south. A positive note is that, compared to many of the 

world’s temperate-zone rivers, many parts of the UMRS still retain the underlying features that 

defi ne river ecosystem integrity, such as a fairly natural discharge regime, ability to move sediments 

through most dams, a nearly complete species complex, and fairly good water quality. These 

features are most evident in the Upper Impounded Reach where habitat diversity is greatest and 

the river maintains more of its connection to the fl oodplain. However, sedimentation and nutrient 

levels are a problem throughout much of the system. Comparing among reaches, suspended solids 

are consistently high in lower reaches but are declining in Pools 4 and 8 (Figure 2.6); submersed 

aquatic vegetation is virtually absent from the lower reaches (Figure 2.15); aquatic invertebrates 

associated with soft sediments are much less abundant in lower reaches (Figures 2.16 and 2.17); 

the percentage biomass of nonnative fi shes is high system wide but is declining (i.e., improving) 

in the upper reaches (Figure 2.24); the abundance of recreational fi shes is declining in La Grange 

Pool and the Open River Reach (Figure 2.25); and isolation of the fl oodplain from the river is much 

more prevalent in the lower reaches (Figure 2.14). Some of these conditions may be associated 

with natural gradients within the river system, but in general, the LTRMP data show more impaired 

ecological condition in the lower reaches relative to the upper reaches. Rehabilitating the system 

will require effort in all reaches; however, the challenges appear to be more daunting in the lower 

reaches as many of the stressors and drivers are more highly modifi ed there.

Refi ning Ecosystem Indicators

This report is an initial comparison of conditions over space and time within the UMRS 

based on data from the LTRMP. The indicators included represent only a few of many that could 

be developed. Potential new indicators can be initially assessed through additional analyses of 

data from LTRMP and other sources. In addition, this report provides critical baseline information 

for helping set management objectives and for making effective decisions about options for 

river management. River managers should seek to strengthen linkages among ecosystem goals, 

ecosystem objectives, and ecosystem indicators. Addressing these issues is not simply a matter 

of data analysis, but requires discussion and consensus among river stakeholders, managers, and 

scientists. 

The Future Role of the Long Term 

Resource Monitoring Program

The LTRMP has developed one of the most extensive and comprehensive data sets on any 

large river system in the world. The early years of the program were devoted to developing the 

infrastructure and methods to collect data in a consistent manner over space and time. That system 

is now in place and operating effectively. Although we should always be searching for ways to 

improve the effi ciency of the program, any changes should consider the integrity of existing data 

and seek to maintain or enhance our ability to detect trends, identify cyclical phenomenon, and 

assess success at rehabilitating the system. 

To manage effectively, managers must improve their understanding of how the UMRS 

functions and reduce uncertainty in their ability to predict the effects of management actions. To 

help achieve this, the LTRMP database provides a unique resource for analyses that can identify 

patterns and relations among components, quantify dynamics of critical variables, and provide 

inputs for developing computer models. This information can be directly incorporated into 
10

management actions and question-driven scientifi c investigations. Results of analyses become 

the basis for designing focal studies to answer specifi c questions and fi eld experiments to test 

hypotheses about system function in an adaptive management context. These fi eld experiments can 

be implemented through habitat rehabilitation projects as part of the EMP.

 A well-designed monitoring program is the fi rst step in documenting efforts toward improving 

the ecological integrity of large ecosystems. The LTRMP stands as a national leader in developing 

and implementing a successful multi-partner collaboration that transcends traditional geo-political 

boundaries that often hamper environmental programs. Historical observations and current LTRMP 

data clearly indicate that the UMRS has been changed by human activity in ways that have 

diminished the ecological integrity of the river. The LTRMP data indicate that status and trends 

differ among regions, and we expect that regional responses to various ecological rehabilitation 

techniques will differ as well. The scientifi c evidence provided in this report indicates that the river 

requires further rehabilitation and continued monitoring. The continuing role of the LTRMP will 

be to provide the data needed to assess the results of management actions and how these changes 

should be viewed in the context of the ecological integrity of the river system.
11

Chapter 1. Introduction

1.1 The Upper Mississippi River System 1.2 Purpose and Scope of the Status and 

Trends Report The Upper Mississippi River System 

(UMRS) is a unique economic, environmental, The initial Status and Trends Report 

and recreational resource. The UMRS basin (U.S. Geological Survey [USGS] 1999) provided 

drains 189,000 square miles and includes major a thorough introduction to the UMRS including 

portions of fi ve states (Minnesota, Wisconsin, extensive descriptions of historical context, 

Iowa, Illinois, and Missouri; WEST 2000). watershed geology and land use, fl oodplain 

The UMRS is one of a small number of large forests, bird populations, water quality, fi shes, 

river fl oodplain ecosystems still characterized aquatic vegetation and macroinvertebrates. In 

by annual fl ood pulses that advance and retreat doing so, that report provided the background 

over the fl oodplain and temporarily expand information upon which the present report 

backwaters and fl oodplain lakes (Sparks et builds. The present report is more focused, 

al. 1998; Gutreuter et al. 1999). The UMRS more quantitative, and incorporates substantial 

provides habitat for a wide array of fi sh and new Long Term Resource Monitoring Program 

wildlife species distributed among a complex (LTRMP) data. The purpose of the report is to 

arrangement of fl owing channels, fl oodplain provide a concise summary of the recent status 

lakes, backwaters, wetlands, and fl oodplain of, and trends in, selected indicators of the 

forests (Patrick 1998). The river supports a ecological condition of the Upper Mississippi and 

diverse mussel fauna, contains more than 25% Illinois Rivers as observed through data collected 

of North America’s freshwater fi sh species, for the LTRMP. It focuses on a quantitative 

and is an internationally recognized fl yway description of biological, physical, and chemical 

for migrating birds (Upper Mississippi River indicators of river health using 9–12 years of 

Conservation Committee [UMRCC] 2000). LTRMP data. Describing the status (range of 

The UMRS has been interlaced with the conditions observed) and trends (change in a 

economy and culture of the basin for thousands consistent direction over time) observed over 

of years (Fremling 2005). Currently, the services this period provides critical information on water 

the river provides include a navigation system quality, biota, and landscapes in the UMRS. 

that transports much of the country’s agricultural 1.3 The Ecosystem of the Upper Mississippi exports, commercial and recreational fi shing, River System drinking water for many communities, and 

a variety of recreational activities, including The UMRS, as defi ned by Congress in the 

10 National Wildlife Refuges within its Water Resources Development Act of 1986, 

boundaries (UMRCC 2000; U.S. Fish and includes the Upper Mississippi River (UMR) 

Wildlife Service 2006). from Minneapolis, Minnesota, to Cairo, Illinois 

Like other large rivers, the UMRS serves (854 river miles); the Illinois Waterway (IWW) 

a diversity of roles and presents signifi cant from Chicago to Grafton, Illinois (327 miles); 

management and conservation challenges. There and navigable portions of the Minnesota 

is a need for regular quantitative assessment of (15 river miles), St. Croix (24 river miles), 

the condition of the river to improve the design Black (1 river mile), and Kaskaskia Rivers 

of conservation and management plans and (36 river miles; Figure 1.1). The Missouri 

evaluate their effectiveness. This report addresses River, which fl ows into the Mississippi River 

that need by providing extensive information just below St. Louis (Figure 1.1), was not 

about the current status and trends in ecological included in this Congressional defi nition of the 

conditions of the UMRS. UMRS. The UMRS encompasses a total area of 

approximately 2.6 million acres of land and water 

in public and private ownership. This includes 
12

the fl oodplain and all associated aquatic and to divert the discharge of Chicago’s sewage from 

terrestrial habitats that are critically important to Lake Michigan to the Illinois River. Initially 

large river ecosystems. completed in 1900, this modifi cation has ongoing 

The geomorphology of the UMRS changes implications for the IWW, including elevated 

substantially along its course, generating water levels and nutrient concentrations and 

longitudinal differences in river characteristics. invasive species exchanges between the UMRS 

The overall profi le of the UMRS can be and the Great Lakes.

divided into 12 reaches (10 UMR reaches; 2 In addition to the internal modifi cations 

IWW reaches) based on geomorphology (U.S. to the UMRS to create the 9-foot navigation 

Army Corps of Engineers [USACE] 2000; channel, its drainage basin has experienced 

WEST 2000). In regional discussions of the considerable change. Beginning around 

river, these 12 reaches are often aggregated to 1840, land use in the basin of the UMRS was 

4 major reaches based on general geomorphic fundamentally altered by intensive farming and 

and ecological considerations (USGS 1999; forestry (Fremling 2005). Vast pine forests of 

Koel 2001; Chick et al. 2006). These reaches northern Wisconsin and Minnesota were nearly 

are (1) the Upper Impounded Reach, (2) the logged in their entirety between 1835 and 

Lower Impounded Reach, (3) the Unimpounded 1915. The conversion of land from prairie and 

Reach, and (4) the Illinois Waterway (Figure 1.1; savannah to agriculture substantially increased 

Box 1.1). soil erosion and sediment input to the UMRS. 

Wetlands were drained and other vegetation 1.3.1 Historical Conditions that slowed runoff was removed to increase the 

Prior to European settlement, the UMR was land available for farming. These changes, along 

broad and shallow and consisted of extensively with stream channelization and urbanization, 

braided channels fl owing past countless increased the speed with which runoff reached 

islands (Fremling 2005). Abundant leaning the UMR, which increased the stage height 

and fallen trees (snags) provided habitat for a and duration of fl ooding. River stage at high 

diverse fl ora and fauna. However, the shallow discharge has been further magnifi ed in some 

water and abundant snags severely impeded places by channel training structures and levees 

navigation and from 1866 through 1940 the constructed to facilitate agriculture on the broad, 

river was fundamentally altered by a series of fertile fl oodplains, primarily south of Rock 

modifi cations to make large-scale commercial Island, Illinois (UMRCC 2000; Pinter 2005a; 

navigation possible. Initial efforts to facilitate Pinter et al. 2006). 

navigation consisted of removing overhanging From the early 1900s through the mid-1970s, 

trees and snags and dredging (Anfi nson 2003). the UMRS suffered extensive pollution from 

Channel training structures, such as wing dams inadequately treated municipal and industrial 

and closing dams, were subsequently added to wastewater. For example, low dissolved oxygen 

increase the depth of the main channel. By 1940, concentrations, large fi sh kills, mussel die-offs, 

construction of a series of 29 locks and dams was and the disappearance of burrowing mayfl ies 

completed between Minneapolis, Minnesota, and (Hexagenia spp.) were documented below 

St. Louis, Missouri, creating a 9-foot navigation Minneapolis, Minnesota (U.S. Environmental 

channel for the length of the UMR. Below St. Protection Agency [USEPA] 2000b). Prior to 

Louis, “open channel” techniques, such as stone wastewater treatment improvements in the 1950s, 

dikes, bank revetment, and dredging have been the Illinois River was degraded to the point that 

used to maintain the navigation channel. most native plants and animals were eradicated 

Similar modifi cations were made to the IWW for more than 100 miles downstream of Chicago 

where eight navigation dams were constructed (Starrett 1972). Recognition of the human health 

during the 1930s as part of the 9-foot channel and safety risks of pollution prompted signifi cant 

project. The IWW was also connected to Lake environmental regulations (e.g., Water Pollution 

Michigan via the Chicago and Des Plaines Rivers Control Act of 1972) and improvements in 
13

Figure 1.1. Map of the basin of the Upper Mississippi River System (UMRS) showing the four major geomorphic reaches and their 

watersheds, locations of navigation dams, and the six study areas for the Long Term Resource Monitoring Program. The UMRS was 

defi ned by legislation and does not include the Missouri River, which joins the Mississippi River just below Pool 26. 
14

Box 1.1. Descriptions of the Four Major Floodplain Reaches Composing the Upper Mississippi River System.

Upper Impounded Reach 

1. Extent: Mississippi River Pools 1-13.

2. LTRMP focal areas within the reach: Pools 4, 8, and 13.

3. Geomorphology: island-braided channels, islands are relatively common. 

4. Effect of locks and dams: substantially expanded the extent of surface waters in most navigation 

pools by creating large impoundments.

5. Levee extent: Relatively few levees. Floodplain generally remains hydrologically connected to the 

river.

6. Floodplain characteristics: narrow (1–3 miles); high proportion of public land (e.g., USFWS National 

Wildlife and Fish Refuge) that supports forests, wetland, and other high quality habitats; Urban development in some fl oodplain areas. 

7. Backwater areas: Abundant.

Lower Impounded Reach 

1. Extent: Mississippi River Pools 14–26. 

2. LTRMP focal area within the reach: Pool 26.

3. Geomorphology: Variable. Pools 14–16—a narrow gorge; Pools 17–26—spread out into a broad 

fl oodplain.

4. Effect of locks and dams: stabilized depth of navigation channel but because of levees, did not 

greatly expand surface waters in most of the reach. 

5. Levee extent: approximately 50% of the fl oodplain is isolated behind levees. 

6. Floodplain characteristics: broad fl oodplain (5–7 miles) below Pool 16; area behind levees has largely been converted to agriculture; riparian forests and forested islands persist riverward of the levees.

7. Backwater areas: Fewer than Upper Impounded Reach.

Unimpounded Reach 

1. Extent: Below Chain of Rocks dam (River mile 203) to the confl uence with the Ohio River (river 

mile 0).

2. LTRMP focal area within the reach: Open River Reach located between river miles 80 through 29 

(near Cape Girardeau, Missouri).

3. Geomorphology: Largely a single main channel constrained by training structures with side channels 

of varying habitat quality.

4. Effect of locks and dams: There are no locks and dams. The navigation channel is maintained solely 

with channel training structures (e.g., stone dikes, closing structure, etc.) and dredging that have 

substantially modifi ed this river reach. 

5. Extent of levees: The main stem levees are large and isolate more than 67% of the fl oodplain except 

during the most extreme fl oods. 

6. Floodplain characteristics: Original fl oodplain is broad, up to 50 miles wide near the confl uence with 

the Ohio River; the fl oodplain is predominately agricultural except for a narrow riparian corridor 

between the levees and river channel and a few aquatic habitat patches within agricultural levee 

districts.

7. Backwater areas: Few.

Lower Illinois River Reach 

1. Extent: Chicago, Illinois, to confl uence with Mississippi River.

2. LTRMP focal area within the reach: La Grange Pool.

3. Geomorphology: Lower river is low gradient, with an average fall of 1.8 inches per mile; consists of 

channels, backwaters, managed wetlands and a broad fl oodplain. 

4. Effect of locks and dams: infl uence is limited by the exceptionally long pools in lower river.

5. Extent of levees: Most of the lower pool fl oodplain areas are leveed. 

6. Floodplain characteristics: Broad fl oodplain dominated by agriculture.

7. Backwater areas: Abundant, but many are separated from the channel by levees.
wastewater treatment since the 1970s. River the aquatic habitats created by lock and dam 

water quality has improved as a result (USEPA construction are aging rapidly. Sediments 

2000b). from upland sources and eroding islands and 

riverbanks are reducing the depth of many 1.3.2 Existing Conditions backwater areas (Bhowmik and Adams 1989; 

The current condition of the UMRS is Rogala et al. 2003). Wind and boat generated 

heavily infl uenced by its agriculture-dominated waves in large open water habitats created by the 

basin and the dams and channel training dams contribute to island erosion and sediment 

structures that regulate fl ow distribution during resuspension (Bhowmik et al. 1992; Chamberlin 

most of the year. In most areas, the landscape, 1994; Knight and Parchure 2004). The resulting 

tributaries, and river are still adjusting to increases in turbidity reduce light penetration 

the changes that have occurred over the last inhibiting aquatic plant production (Korschgen 

150 years. The overall condition of much of 1990; UMRCC 2003; Kreiling et al. 2007). 

the UMR has improved substantially since the Backwater sediments have become increasingly 

1960s due to improvements in sewage treatment unconsolidated because the dams have eliminated 

and land use practices. However, the UMRS the summer low fl ow river stage that historically 

still faces substantial challenges concerning its allowed backwater and shoreline sediments to 

overall condition, including be exposed and compacted (Rogala et al. 1999). 

The unconsolidated sediments are more easily 

• high sedimentation rates in some resuspended, further reducing water clarity. In 

backwaters and side channels (Rogala addition, high water levels have reduced the 

et al. 2003); amount of fl oodplain forests, either by direct 

• an altered hydrologic regime resulting mortality or by creating conditions in much of 

from modifi cations of the river to the fl oodplain that favor wetlands or grasslands. 

improve navigation and modifi cations of Navigation dams also reduce fi sh movement by 

the fl oodplain and basin for agriculture reducing or blocking fi sh passage (Chick et al. 

(Pinter et al. 2006); 2006).

• loss of connection between the fl oodplain Nonnative fi sh species are a substantial 

and the river, particularly in the southern fraction of the biomass, particularly in the 

reaches of the UMRS (see Box 1.1); southern reaches and are a growing problem 

• nonnative species (e.g., zebra mussels for the UMRS (Chick and Pegg 2001; Ickes 

[Dreissena polymorpha] and Asian carp et al. 2005). Zebra mussels and round goby 

Hypophtalmachthys spp.]; Tucker et al. (Neogobius melanostomus), introduced via the 

1993; Chick and Pegg 2001); IWW from the Great Lakes, are also a concern 

• high nutrient and suspended sediment (e.g., Tucker et al. 1993). Sedimentation and 

concentrations (Goolsby and Battaglin excessive nutrient and pesticide runoff continue 

2001); and to be sources of critical ecological impacts in the 

• degradation of fl oodplain forests (Yin main stem rivers. 

and Nelson 1995). The factors affecting water quality concerns 

in the river have shifted since the 1960s and 

The cumulative results of these impacts continue 1970s. Treatment of municipal and industrial 

to affect the ecological integrity of the UMRS wastewater discharges is greatly improved and 

(WEST 2000). these “point sources” contribute much less to the 

Some effects of the navigation locks and nutrient and suspended solid load in the UMRS 

dams were initially perceived as ecologically today than previously. As a result, some aspects 

benefi cial because newly created aquatic habitats of water quality, such as dissolved oxygen 

were quickly colonized by fi sh and aquatic concentrations, have improved substantially, and 

plants, resulting in a short-term increase in sensitive species, such as burrowing mayfl ies 

river productivity (Fremling 2005). However, are again relatively common in much of the 

15
river (USEPA 2000b; Sauer 2004). However, their outcomes have been described extensively 

the intense human land use in the UMRS basin in several reports and publications (e.g., Belanger 

still results in excessive nutrient and sediment et al. 1990; Richardson and Clemment 1993; 

inputs from nonpoint sources such as runoff from Lubinski and Gutreuter 1994; Theiling 1995).

agricultural fi elds and urban areas (Engstrom et The LTRMP component of the EMP is a 

al. 2000; UMRCC 2000; Donner et al. 2004). multipurpose program of monitoring, applied 

research, and management evaluation designed to 1.4 Monitoring and Managing the River: The achieve the following broad goals (USGS 1997): Environmental Management Program

The Environmental Management Program 1. Develop a better understanding of the 

(EMP) was established by Section 1103 of the ecology of the UMRS and its resource 

Water Resources Development Act of 1986. A problems,

fundamental tenet of this program, as stated in 2. Monitor resource change,

the legislation, was the recognition by Congress 3. Develop alternatives to better manage the 

that the UMRS is a “nationally signifi cant UMRS, and

ecosystem and nationally signifi cant commercial 4. Provide for the proper management of 

navigation system” —the only river in the United monitoring information.

States to be formally recognized as such— that 

should be managed to support multiple uses. In support of these goals, data collection, 

The EMP is managed by the U.S. Army Corps of analysis, presentation, and publication are carried 

Engineers and implemented in cooperation with out by the staff of the USGS Upper Midwest 

the fi ve UMRS states (Illinois, Iowa, Minnesota, Environmental Sciences Center (UMESC) and 

Missouri, and Wisconsin) and several Federal six LTRMP fi eld stations operated by staff from 

resource agencies (U.S. Geological Survey, U.S. the UMRS states. Overall Program responsibility 

Fish and Wildlife Service, U.S. Environmental rests with the U.S. Army Corps of Engineers, 

Protection Agency, and the U.S. Department of whereas the USGS UMESC provides science 

Agriculture Natural Resources Conservation leadership and administers the LTRMP. The 

Service). In addition, the EMP works in USGS implements the LTRMP in cooperation 

coordination with a variety of nongovernmental with the conservation agencies of the states 

agencies such as state universities, the Upper of Illinois, Iowa, Minnesota, Missouri, and 

Mississippi River Basin Association, the National Wisconsin, which operate six fi eld stations on the 

Audubon Society, and The Nature Conservancy. river system.

The collaborative relationships among these The LTRMP employs a variety of 

Federal agencies, states, nongovernmental monitoring, data serving, and research efforts. 

organizations, and other stakeholders, including The LTRMP core monitoring program collects 

commercial interests developed by the EMP biological, chemical, and physical data on the 

provide a national model for large-scale river using a variety of fi eld, laboratory, and 

restoration and monitoring work. remote-sensing methods. Monitoring data from 

The EMP consists of two principal the past 12 years have been analyzed using a 

components (1) the Habitat Rehabilitation and diverse array of approaches to improve our 

Enhancement Projects (HREP) and (2) the understanding of the ecology of the UMRS. 

LTRMP. The HREP component of EMP is For example, statistical models have been 

managed by the U.S. Army Corps of Engineers used to determine important predictors of the 

in consultation with the U.S. Fish and Wildlife abundance and distribution of vegetation (Yin 

Service and the natural resource agencies of the and Langrehr 2005), multivariate analyses 

fi ve UMRS states. Through HREP, the Corps and have been used to show how fi sh community 

its partners rehabilitate aquatic habitats degraded composition differs among the study reaches 

by navigation development and other changes to (Barko et al. 2004; Chick et al. 2005; Ickes et 

the river and its basin. Some of these projects and al. 2005), and spatial and temporal patterns 

16
within the UMRS have been analyzed to better et al. 2006). One such approach is to use the 

understand longitudinal patterns in the river and “historical condition” of the river, that is, the 

differences among various aquatic areas (e.g., condition prior to current disturbances (i.e., 

main channel, impoundment, and backwater the condition before agriculture dominated the 

areas; Koel 2001; Sauer 2004; Houser 2005; landscape and navigation channel maintenance 

Ickes et al. 2005). Indicators of ecosystem health dominated the river). However, data on “prehave been analyzed to determine the current disturbance” conditions are limited for most 

condition of the UMRS and how it is changing of the indicators in this report. An alternative 

over time (USGS 1999). The results of this approach is to use “minimally disturbed” or 

research are provided to the management and “least disturbed” areas to determine the goals 

scientifi c community through presentations, for restoration for more degraded parts of the 

324 technical reports, and more than 65 peer- river (Stoddard et al. 2006). Note that these 

reviewed publications (http://www.umesc.usgs. alternative approaches to establishing goals for 

gov/ltrmp.html). Management tools, models, and rehabilitation require extensive data on the river 

information building on this research are also system combined with some agreement on how 

served through the UMESC Web site. to evaluate “best condition.” Thus, evaluating 

The LTRMP data collected on the UMRS, ecosystem health requires (1) identifying and 

including the ecological response to HREP quantifying societal values concerning the health 

projects, have also served as the springboard of the system and (2) measuring indicators that 

for restoration efforts. Design and construction refl ect those values and are expected to respond 

methods, information on habitat response, to management actions. This report focuses on 

monitoring data, interagency coordination, and measuring indicators. The results presented here 

public input mechanisms created by the Program will contribute to discussions among stakeholders 

have informed the development of the ecosystem and managers regarding societal views of 

restoration plan of the Upper Mississippi River ecosystem health. Those discussions should aim 

and Illinois Waterway Navigation Study (USACE to explicitly link fi eld observations of select 

2004) and the main stem component of the ecosystem attributes to stakeholder values. 

Illinois River Basin Restoration Comprehensive 1.6 Ecological Drivers, Stressors, and Plan (USACE 2006a). Indicators

1.5 Desired Future Conditions: Providing the Attempts to link fi eld observations to Foundation for Developing Objectives stakeholder values often benefi t from developing 

This information provided in this report is an a conceptual framework. One such conceptual 

essential contribution for the ongoing discussion framework provides a structure for identifying 

of desired river conditions among stakeholders, and evaluating (1) the primary ecosystem drivers; 

managers, and scientists. Central to these (2) stressors imposed upon the system due to 

discussions is the topic of appropriate reference human uses of the system (Figure 1.2); and 

conditions. There are multiple approaches for (3) indicators that can be conceived, developed, 

determining reference conditions that can help and analyzed to inform decision makers in the 

defi ne desired future conditions and set targets management of the system (Box 1.2). U.S. 

for ecosystem rehabilitation (Stoddard et al. Geological Survey (1999) provided the initial 

2006). Ideally, a similar but undisturbed river conceptualization of the drivers and stressors 

would serve as a reference system against which approach to indicator development and provided 

the UMRS could be compared (Hughes et al. considerable information and detail concerning 

1986). For large, unique ecosystems, such as historical and contemporary drivers and stressors 

the UMRS, there are no suitable “reference” acting upon the UMRS. 

systems, but there are alternative approaches 

that use a subset of the data from the UMRS to 

determine the “reference” condition (Stoddard 

17
1.6.1 Indicator Development indicators. Sampling methods are standardized 

for each component (Gutrueter et al. 1995; Thiel The balance of this report focuses on and Sauer 1999; Yin et al. 2000; Soballe and presenting quantitative indicators developed Fischer 2004) permitting rigorous comparisons from LTRMP data sources and expected to refl ect between locations and over time. Also, the UMRS ecosystem health as described in the LTRMP staff collects data on land cover and fi rst Status and Trends report (USGS 1999; see bathymetry for the entire UMRS, permitting Chapter 2). In Chapter 3, information presented the development of landscape indicators and in Chapter 2 is integrated into an overall comparisons with biological and chemical ecosystem health evaluation. indicators. 

Data Sources Indicator Selection and Analysis The LTRMP intensively samples four Scientists within LTRMP, in conjunction with primary ecological components (fi sheries, the EMP partnership, identifi ed 24 ecosystem water quality, aquatic vegetation, and aquatic indicators to include in this report (Table 1.1). macroinvertebrates) from six 30–60 mile river The indicators are divided into six categories sections that traverse the geomorphic and human and can be related to previous documents and disturbance gradients described in Section 1.3.1 to system stressors (Fig 1.2). These selected (Figure 1.1). Data are collected using a random indicators derive from a broader pool of potential sampling design, permitting unbiased evaluation indicators monitored by LTRMP. Collectively, of selected biological, chemical, and physical 

18

Figure 1.2. Human stressors on the Upper Mississippi River ecosystem (WEST 2000; USACE 2004). 

Release of pollutants to atmosphere Global Warming

Non-point source

loadings

Point source

discharges

Point source

discharges

Thermal discharges

Floodplain forest management

Commercial exploitation

Sport exploitation

Exotic species

Headwaters impoundments

Channelization of stream

drainage network

Tiling, ditching, wetland

drainage

Impoundment, river regulation

Levees, floodplain damage

Habitat restoration, protection

Managed floodplain impoundments

Dredging, material placement

Channel training strucures

Towboat entrainment

Powerplant entrainment

Land Use

Weather and Climate

BASIN SCALE AND LARGER

WITHIN UMRS BASIN

WITHIN UMRS MAINSTEM,

RIVERS, AND FLOODPLAINS Water Quality Hydrologic Regime

Pattern of River

Habitats

Abundance and Diversity

of Plant and Animal

Populations
19

Box 1.2. Conceptual Defi nitions of Drivers, Stressors, and Indicators.

Drivers are the major external forces that have large-scale infl uences on ecosystems. For example, they 

affect disturbance regimes (e.g., fl oods and droughts), material transport and fl ux (e.g., nutrients and 

sediments), and production potential. Examples in the UMRS include geology, climate and hydrology 

(Figure 1.2).

Stressors are physical, chemical, or biological changes that exceed the natural assimilative capacity of the 

ecosystem. Stressors can cause signifi cant changes in biological communities, ecosystem function, and 

ecosystem services at various scales (e.g., local, watershed, regional, basin). Stressors may be of natural or 

human origins; both are important in the contemporary UMRS ecosystem. Examples of natural stressors 

may include physical or biological responses to fl oods (e.g., erosion, sediment suspension, or fl oodplain 

forest mortality), and physiochemical responses to drought (e.g., low oxygen levels, thermal stress). 

Examples of human made stressors may include excessive nutrient inputs associated with past and present 

land use decisions (e.g., agricultural fertilizers and waste treatment effl uent), invasive species, and altered 

hydrology arising from the combined effects of river impoundment, system engineering for commercial 

navigation, and/or fl ood control measures (Figure 1.2).

Indicators are selected attributes or elements of the system that are (1) sensitive to system drivers and 

stressors, and (2) sensitive to management efforts to mediate undesirable ecosystem conditions. Thus, 

indicator selection and development depends upon (1) identifying relevant drivers and stressors; (2) 

selecting ecosystem indicators that are sensitive to primary drivers, stressors, and management actions; 

and (3) generating quantifi able statements concerning societal values that identify both “healthy status” 

and “actionable trends” in selected indicators. Such quantifi able statements on societal values are often 

termed “benchmarks” or “endpoints” and are crucially important to defi ne. Generalized examples of 

indicators include population levels (e.g., number of bluegill or the amount of nutrients or pollutants), 

biotic community metrics (e.g., biomass of nonnative species, number of fl oodplain dependent species, 

proportion of pollution tolerant species, or fl oodplain forest community composition), or metrics of 

ecosystem processes (e.g., biological production rates, sedimentation rates, and nutrient assimilation 

rates).

the intent of the selected indicators is to provide quantitative targets, which are used in indicator 

an assessment of the current health of the UMRS. evaluation. However, few regulatory standards 

In Chapter 2, each indicator is evaluated for currently exist for indicators of ecosystem health 

differences in indicator status across locations for the UMRS. Thus, for most of the indicators, 

within the UMRS and for trends over time comparisons within the UMRS are used to 

(9–12 years). When possible, annual estimates identify areas that were “better” or “worse” 

of uncertainty for each indicator (represented than other areas in the river. In some instances, 

as error bars around each annual estimate), and indicators were correlated with suspected drivers 

uncertainty in trends (represented by curves or stressors, or with information from recent 

bounding a best fi t trend line), were calculated research studies, to more clearly link system 

(Cochran 1977; Gutreuter et al. 1995). responses and relations. However, the collective 

This report makes use of several approaches knowledge base is currently too incomplete to 

to evaluate the selected indicators. There are determine causes for the patterns observed in 

a few instances wherein historical data were most indicators.

accessible in published reports and these data 1.6.2 Linking Ecosystem Goals, Objectives, and are discussed in the evaluation of the indicator Indicators (e.g., total nitrogen, depth diversity). For a few 

indicators (e.g., total nitrogen, total phosphorus), Whereas ecosystem indicators convey 

regulatory agencies have recommended specifi c quantitative information on ecosystem 
condition, ecosystem goals and objectives Ecosystem Goals

convey information concerning how society Informally, broad goals for ecosystem health 

values ecosystem condition. Clearly articulating have been adopted by many river managers 

such value-based perspectives on a system as and scientists over time, but no common set of 

large, diverse, and complex as the UMRS is goals and objectives has been formally adopted 

exceedingly diffi cult, yet critically important. by stakeholders. Still, many ecosystem goals 

for the condition of the UMRS ecosystem 

20

Table 1.1. Ecological context of indicators derived using data from the Long Term Resource Monitoring Program (LTRMP) and their 

relation to previous documents. 

Ecological Health Criteria Indicator 

Characteristic UMRCCa

 (2001) (USGSb 1999) Category LTRMP Indicator

Hydrology More natural Floodplain Hydrology Mean annual discharge

hydrograph; Flow connectivity; Seasonal water elevation

distribution on Value of natural 

fl oodplain disturbances

Water Quality Improve water Function as part Water Quality Major nutrients

quality of a healthy 

basin;

Viable 

Chlorophyll a

Total suspended solids

populations Dissolved oxygen

Suitable winter habitat for 

sunfi shes

Habitats Reduce sediment Ecosystem Sedimentation Depth diversity in impounded 

impacts; Restore sustainability; areas

natural fl oodplain; Viable Net sedimentation in backwaters

Connect backwaters; populations

Side channel, island 

habitat Viable 

populations;

Land cover/Land 

use

Floodplain forest

Emergent vegetation

Floodplain 

connectivity

Area of fl oodplain behind levees

Abundance and Restore natural Viable Aquatic Vegetation Submersed aquatic vegetation

Diversity fl oodplain; Provide 

fi sh passage at dams;

Monitor exotics

populations Macroinvertebrates Burrowing mayfl ies 

(Hexagenia spp.)

Fingernail clams 

(Musculium transversum)

Fisheries Bluegill 

(Lepomis macrochirus)

Channel catfi sh 

(Ictalurus punctatus)

Sauger (Sander canadense)

Smallmouth buffalo 

(Ictiobus bubalus)

Forage fi sh index

Species richness

Nonnative fi shes

Recreationally harvested fi shes

Commercially harvested fi shes

a

UMRCC = Upper Mississippi River Conservation Committee

b

USGS = U.S. Geological Survey
have been proposed in various management provide a qualitative or quantitative statement 

proposals and plans, particularly as related to that describes desired future conditions against 

the abundance and distribution of habitat. There which indicators can be evaluated for progress or 

are ongoing collaborative efforts to set goals and attainment.

objectives for the UMRS ecosystem that include Ecosystem Objectives participation of the stakeholder community There have been at least two previous and (The Nature Conservancy 1998; UMRCC 2000; extensive efforts to defi ne ecosystem objectives USACE 2000, 2004; Lubinski and Barko 2003; for the UMRS. The Habitat Needs Assessment U.S. Fish and Wildlife Service [USFWS] 2006). (HNA; Theiling et al. 2000) was the fi rst Six criteria of ecosystem health for the multiagency sanctioned effort by the scientifi c UMRS were stated in the 1998 Status and Trends 

community to set objectives for aquatic and Report (USGS 1999). These six criteria comprise terrestrial habitat protection and restoration for three general criteria identifi ed for their value in 

the UMRS. The HNA focused on identifying characterizing basic ecosystem health (Criteria the desired future mix of habitats throughout 1–3 below; Grumbine 1994) and three additional the UMRS. Resource managers and scientists criteria developed specifi cally for fl oodplain indicated that the future should be characterized rivers (Criteria 4–6 below). Collectively, these by improved habitat quality, habitat diversity, six criteria formed the basis of the fi rst ecosystem and a closer approximation of predevelopment health evaluation for the UMRS. 

hydrologic regime. River regulation, 1. The ecosystem supports habitats sedimentation, and fl oodplain development were and viable native animal and plant rated as the primary stressors affecting river populations similar to those present habitats (Theiling et al. 2000). A similar effort before any disturbance. is now needed concerning the desired future 2. The ecosystem is able to return to its pre- condition of water quality and biotic diversity existing condition after a disturbance, and abundance. whether natural or human-induced. 

Shortly after publication of the fi rst Status 3. The ecosystem is able to sustain itself. and Trends report in 1999 (USGS 1999) and 4. The river reach functions as part of a building on the HNA (USACE 2000), the Upper healthy basin. Mississippi River Coordinating Committee 5. The annual fl ood pulse connects the main (UMRCC) proposed nine river ecosystem channel to its fl oodplain. objectives. These objectives addressed 6. Infrequent natural events, such as fl oods 

management needs to sustain and restore the and droughts, are able to maintain structure and function of the UMRS (UMRCC ecological structure and processes within 2000). These objectives were the reach. 

1. Improve water quality for all uses; In their broadest sense, these criteria 2. Reduce erosion and sediment impacts; refl ect ecosystem conditions valued by society. 3. Restore fl oodplains to allow channel For example, Goal 1 ensures natural heritage meanders and habitat diversity; conservation, sustainable consumptive uses 4. Provide for seasonal fl ood pulses and of river biota (e.g., hunting and fi shing), and periodic low fl ows to improve nutrient sustainable nonconsumptive uses (e.g., boating, base, plant growth, and succession; photography, and bird watching). Note, however, 5. Enable connectivity of backwaters to the that some goals, such as Goal 3, are unlikely to main channel; and be reached in the foreseeable future for a heavily 6. Provide for opening of side channels, managed system, such as the UMRS. Such create islands, shoal and sandbar habitat. ecosystem goals provide a vision for desired 7. Improve channel maintenance and future conditions, but they lack specifi city dredge disposal practices in ways that about how to achieve that vision. Therefore, support ecosystem objectives. objectives must be explicitly stated. Objectives 

21
8. Sever pathways of exotic species developing a process to evaluate ecosystem 

introductions and spread within the health on the UMRS. Management authority 

UMRS. is spread among several Federal and state 

9. Provide native fi sh passage at dams. agencies, each with a different management 

mandate. These different mandates will need to Linking Goals, Objectives, and Indicators be both reconciled and accommodated in future 

Past attempts to develop goals and objectives evaluations of ecosystem health. Indicators must for the UMRS ecosystem proceeded without then be reassessed or revised to better align them benefi t of the information provided by this with ecosystem objectives such that they permit report. This synthesis of LTRMP data provides tracking progress toward attaining desired future basin scientists, managers, and stakeholders conditions.

with an unprecedented opportunity to further To this end, the EMP provides a base of 

refi ne ecosystem health evaluations for the fi eld science and management capability that is UMRS. In doing so, partnering agencies and critical to defi ning, developing, measuring, and individuals should seek to strengthen linkages meeting ecosystem objectives for the UMRS. among ecosystem goals, ecosystem objectives, The management experience gained through and ecosystem indicators. Addressing these HREP activities, and the technical capabilities issues is not simply a matter of data analysis, but developed through LTRMP activities, provide a requires discussion and consensus among river solid foundation upon which to further develop, stakeholders, managers, and scientists. evaluate, and track progress toward UMRS Achieving consensus on ecosystem ecosystem health objectives. objectives may be the most diffi cult part of 

22
Chapter 2. Status and Trends of Resources in the Upper Mississippi 

River System

2.1 Introduction • A description of future pressures 

that may affect levels and trends of This chapter contains information on various the indicator along with potential indicators of ecosystem condition. It begins with management actions; and a discussion of two indicators of river hydrology • Graphs of data available. using data collected by the U.S. Army Corps 

of Engineers and U.S. Geological Survey at These data provide a baseline of information 

long-term gaging stations within the system. on levels and trends for each indicator. The 

The remaining 22 indicators use data collected process of developing indicators for large rivers 

by the LTRMP at fi ve sampling areas on the is in its infancy, however, and for most of the 

Upper Mississippi River (UMR) and one on indicators in this report, there is little information 

the Illinois River (Figure 1.1). Each indicator is on what levels are appropriate in large rivers. We 

displayed for those sampling locations with data have suggested some levels based on information 

available. Not all locations were sampled for from the literature, but any attempt to defi ne 

every indicator. Most indicators present annual specifi c levels should consider the concerns and 

data from the main period of LTRMP sampling needs of river users and the large variability 

under current methods (early 1990s through over space and time evident in all large rivers. 

about 2004). Data for sedimentation and land Acceptable levels may be different in different 

cover are comparisons at one or more points parts of a river or in different seasons. 

in time derived from more intensive sampling This report is an initial attempt to compare 

efforts. Assessments of condition are made conditions over space and time within the UMRS 

across sampling locations and across the four based on data from the LTRMP. Most of these 

main geomorphic reaches (see section 1.2) when data were collected from multiple locations 

appropriate. The sampling design and techniques throughout the system that encompass a wide 

used for each component are documented on the range of underlying drivers and stressors. 

LTRMP web site at http://www.umesc.usgs.gov/ The baseline information derived from these 

ltrmp.html. data is critical for helping set management 

objectives and for making effective decisions Each indicator is presented with about options for river management. Future 

• An assessment of the status and trends information will build upon these data to show 

for the period covered; changes in condition of the river over time and 

• A description of the purpose and to look at long-term dynamics, such as cycles of 

importance of the indicator; abundance. Many of these indicators are linked 

• An assessment of the state of the by various processes and interactions at work in 

ecosystem relative to that indicator with the river ecosystem. We discuss some of those 

historical context, when known; linkages, but this is a fertile area for additional 

analyses and research.

23
24

2.2 River Hydrology Indicators For these indicators, we identifi ed 

four gaging stations with suffi cient data to 

Rivers are inherently fl owing water systems. examine water elevations before and after 

A river’s hydrology, or fl ow dynamics, integrate dam construction and discharges since 1950 the effects of climate, land forms, land use, (Table 2.1). For elevation data, the pre- and river management. Periodic changes in the dam period for the Mississippi River sites amount of fl ow and in water elevations are key began between 1861 and 1888, depending on elements of a river’s hydrology. Flowing water availability of data, and ended in 1929. On the transports dissolved and suspended materials Illinois River, the preconstruction period was continually within channels and periodically 1885–1899 because in 1900 the river system within the fl oodplain as the river fl oods, then was modifi ed by a diversion channel from Lake drains off-channel areas. Changes in water Michigan at Chicago. Postconstruction dates elevation result in changes in water depth and begin in 1940 except for the St. Louis site where wetted area. Plants and animals in the UMRS 1960 was used to account for construction of 

have adapted to a natural regime of relatively storage reservoirs on the Missouri River (which predictable seasonal and annual changes in fl ow enters the Mississippi River above St. Louis). and water elevation. In the UMRS, hydrology These data provide historical context for the has been affected by changes in both the hydrologic conditions existing during 1993– watershed and channel, including changes in 2004, when the LTRMP data used in this report land cover (especially conversion to agriculture, were collected. 

loss of wetlands, and drain tiling of farm fi elds) 

that increased runoff, construction of dikes 2.2.1 Mean Annual Discharge

in channels and levees on the fl oodplain that 

constrict fl ows, and construction of dams on Assessment

the UMRS in the 1930s that increased water Status: Good. The range of annual 

elevations. The indicators chosen for hydrology discharges throughout the UMRS is similar to 

were annual discharge and the seasonal pattern of historical ranges.

water elevations.

Table 2.1. Gaging stations on the Upper Mississippi River System used for analyses of elevations and discharge. 

River Years used for elevation datac

Station name Station codea Location mileb Pre-dam Post-dam

Mississippi River

Control point of 1888–1903 Winona, Minnesota 05378500 701 1940–2004 Pool 6 1928–1929

Dam 19 Keokuk, Iowad 05474500 352 -- --

Control point of Louisiana, Missourid 0282A 273 1879–1929 1940–2004 Pool 24

St. Louis, Missouri 07010000 Open River 173 1861–1929 1960–2004

Illinois River

Upper portion of Valley City, Illinois 05586100 60 1885–1899 1940–2004 Alton Pool

a

Station codes are from U.S. Geological Survey, except the Louisiana, Missouri, station, which is a Corps of Engineers 

code.

b

River mile on the Mississippi River is above the confl uence with the Ohio River and on the Illinois River is above its 

mouth at the Mississippi River.

c

Years used for discharge data were 1950–2004.

d

The gage at Keokuk, Iowa, was used only for discharge and the gage at Louisiana, Missouri, was used only for elevation. 
Trend: Stable to slightly increasing. Mean conditions on the UMRS, especially in the Upper 

annual discharge increased throughout the Impounded Reach. Within that period, discharge 

system after about 1970, similar to all of the varied substantially with record or near record 

eastern U.S. During 1993–2004, mean discharge fl ows in 1993 and relatively low fl ows in 2000 

increased slightly in the impounded portion of and 2003. In addition, this period followed 

the Mississippi River compared with the previous 3 years of low fl ows in 1987–1989 experienced 

22 years, but was stable in the Unimpounded throughout the system. 

Reach and in the Illinois River. Plants and animals within the UMRS are 

constantly adapting to changing fl ows. High Purpose mean annual discharge indicates that biota have Mean annual discharge is a measure of the faced generally wetter conditions in recent years. average amount of water fl owing through a river However, extreme discharge events occurring in any one year. It integrates the effect of fl ood over short periods may create unusual conditions fl ows and low fl ow periods within each year. that can have substantial effects on a variety of Changes in fl ow affect a variety of physical ecological processes. A combination of analyses processes and features, including transport of of LTRMP data, which are collected annually, waterborne materials (sediments, nutrients, etc.), and focused research studies that investigate water depths, the total amount of aquatic area, short-term changes produced by extreme events, access to fl oodplains, current velocity, scouring, should help reveal linkages between discharge and retention time of water, all of which can and ecological processes. affect ecological processes and abundance of 

biota. Future Pressures

Building of additional dams that would State of the Ecosystem affect discharge on the UMRS or its tributaries is Dams on the UMRS were built mainly to unlikely. Substantial changes in annual discharge facilitate commercial navigation. They were not are not expected in the near future, but in the designed for fl ood control and have little storage long term, discharge on the UMRS will be linked capacity. Thus, these dams have little effect on mainly to climate. Predictions of how climate total discharge (Chen and Simmons 1986; Sparks change might affect the UMRS are diffi cult 

1995), which is managed on a run-of-the-river because of the variety of interacting factors basis (Landwehr et al. 2005). Large changes in involved and the multiple scales at which they discharge associated with rivers dammed for operate. These factors include total amount and storage reservoirs (e.g., Colorado River) are not timing of rainfall, number and timing of extreme evident on the UMRS. events, temperature effects on snowmelt and The UMRS has experienced increased evaporation, potential changes in land cover discharge since 1970 (Figure 2.1). This increase in the watershed, and changes in ground water appears to be part of a broader trend that affected tables. Climate change models are uncertain the entire eastern United States (McCabe and regarding whether mean annual precipitation Wolock 2002). After 1970, the discharge during and discharge will change in the UMRS basin, years of low fl ow was similar to that observed but the region is expected to see more variability during 1950–1969, but there were more years in precipitation (Kundzewicz et al. 2007). of high discharge. Thus, the mean and range of Global effects on climate change are outside the discharges during 1970–1992 were higher than direct control of UMRS managers. However, if for 1950–1969 at all locations. During the period changes in discharge occur, managers will need 1993–2004, when the LTRMP data used in this to develop strategies that can be applied to the report were collected, fl ows were slightly higher watershed and the UMRS to either maintain 

than 1970–1992 in the Impounded Reaches of critical ecological processes or adapt to changes the UMR, but were similar on the Illinois River in those processes in ways that will allow the and the Unimpounded Reach. Thus, the period 

1993–2004 was generally wetter than historical 

25
Figure 2.1. Mean annual discharge (1,000s of cubic feet per second) on the Upper Mississippi River System from 1950 to 2004 for 

gages at Winona, Minnesota; Keokuk, Iowa; and St. Louis, Missouri, on the Mississippi River and Valley City, Illinois, on the Illinois River. 

Horizontal lines on the graphs indicate mean discharge during 1950–1969, 1970–1992, and 1993–2004. 

26
river to continue to provide the ecological goods reaches has been to effectively remove the 

and services desired by the public. lower water elevations experienced during the 

pre-dam period. This has two primary effects, Authors permanently inundating the area immediately Robert Gaugush and Barry Johnson. behind each dam and reducing current velocities 

2.2.2 Seasonal Cycle of Water Elevation behind the dams. Reduced current velocities 

promote increased sedimentation rates and 

Assessment fi lling of impounded areas and backwaters. 

The permanently inundated areas no longer Status: Fair to Poor. All reaches have 

experience the annual cycle of wetting and maintained seasonal cycles with spring fl ooding. drying that existed before dam construction, In the impounded reaches, mean water elevation which has resulted in substantial losses of aquatic is higher than pre-dam levels, especially during vegetation along shorelines and in shallow low fl ow periods. In the Unimpounded Reach, wetland areas. In addition, the open expanses water elevations are similar to historical levels. 

of water above dams are now subjected to the Short-term variation in elevation is also a 

erosive force of wind-induced waves, which has concern in all reaches. 

resulted in loss of islands and fi lling of deeper Trend: Stable. There are, however, areas by sediment in these zones. The physical opportunities for improvement with management changes in hydrology produced by the dams were strategies that allow lower water levels during essentially immediate. The resulting geomorphic low fl ows in many impounded reaches, which changes (loss of islands and reduced depth may lead to improvements in this indicator in diversity) were probably rapid immediately after those locations. 

the dams were built, but are now occurring at 

Purpose slower rates. 

Plants and animals in the UMRS have In the Unimpounded Reach, the mean annual 

adapted to a relatively predictable seasonal cycle hydrographs at St. Louis were similar between 

of water elevations, which is refl ected in their pre- and post-dam periods and show only 

life history strategies. Changes in the seasonal slight changes in the annual cycle of elevation. 

cycle (timing, increase or decrease in range of This site is not affected by a downstream dam, 

elevations, etc.) can affect a variety of ecological but is affected by other factors (Simons et al. 

functions including access to fl oodplains, 1974). Beginning in the mid-1800s, numerous 

timing of reproduction, drying of soils, seed dikes stretching from the shoreline into the 

germination, and production of plants as food for channel were built throughout the UMRS to 

migrating waterfowl. Annual variation in water force water into the middle of the channel at 

elevation is always evident and biota must adapt low fl ows (Brauer et al. 2005). The dikes in the 

continuously, but this indicator considers the Unimpounded Reach had greater ecological 

average conditions faced by biota over multiple effects than in the impounded reaches. In the 

years and multiple life cycles. Unimpounded Reach, dikes were much longer 

and higher and the area between dikes fi lled with State of the Ecosystem sediment to create dry land. This permanently Annual hydrographs show clear differences constricted the channel and greatly reduced over time between the impounded reaches and the amount of shallow and off-channel aquatic the Unimpounded Reach. In the impounded habitats. This constriction created a narrower reaches, dams have increased water elevations channel with increased water depth and current up to 3 m, primarily during low fl ow periods velocity. Also, in the 1950s, dams constructed (summer and winter, Figure 2.2). These dams on the Missouri River substantially reduced the were not designed for fl ood control and their amount of sediment delivered by the Missouri effect on elevations is much less during spring River to the Mississippi (Meade 1995). The fl oods. The overall effect on the impounded combination of a constricted channel and reduced 

27
28

Figure 2.2. Average annual hydrographs of water elevation (m above mean sea level) on the Upper Mississippi River System before 

dam construction (narrow line) and after dam construction (bold line). Gage locations are Winona, Minnesota, and Louisiana and St. Louis, 

Missouri, on the Mississippi River, and Valley City, Illinois, on the Illinois River. See Table 2.1 for specifi c dates used for each gage. 
sediment delivery resulted in erosion of the allowed managers to reduce water levels during 

Mississippi River bed, which reduced the bed summer (drawdowns) on Pools 5, 8, 24, and 

elevation. Compared to historical conditions, 25. These drawdowns have shown promise for 

the channel in the Unimpounded Reach is now producing ecological benefi ts with little effect 

narrower and deeper, and current velocities have on commercial and recreational users. Managers 

increased. In addition, comparisons of water are using the results of these experiments to 

elevation at identical discharges indicate that begin developing strategies for using drawdowns 

at low discharge, water elevation is lower than as long-term management tools. In addition, 

historically observed and at high discharge is changes in dam operations may allow managers 

higher than historically observed (Wlosinski to reduce short-term variation in water elevations 

1999; Pinter et al. 2001). These changes, by using more frequent changes of dam gates, 

combined with an extensive levee system in the or by managing water levels using a control 

Unimpounded Reach (see section 2.5.3) have point at the dam rather than at mid-pool. The 

greatly reduced the connection of the river to its loss of morphological complexity due to island 

fl oodplain. erosion and sedimentation of deeper areas may 

In addition to seasonal cycles, short-term be partially addressed through management 

(daily to weekly) variation in water levels has actions, such as island construction and dredging. 

also increased substantially within the UMRS Management of land use and land cover in the 

(R. Gaugush, unpublished data). The magnitude watershed to reduce runoff would help to reduce 

of these elevation changes is greater in the lower short-term variation in discharge and water 

reaches. Short-term variation can have negative levels, but actions on the uplands are outside the 

effects on reproduction and survival of many control of managers in the EMP. 

plants and animals that need relatively constant In the Unimpounded Reach, hydrologic 

water levels, especially during critical early life conditions are not expected to change in the 

stages. Factors that increase short-term variation near future. Managers will need to develop 

in water levels include changes in land use that strategies for ecological rehabilitation within the 

increase runoff and result in more rapid delivery constraints of a constricted channel and leveed 

of water to the UMRS. In addition, some dams fl oodplain. Management strategies that create 

on the UMRS are operated to control water more shallow areas within the main channel 

elevations at a point in the middle of a pool, are of particular interest. Side channels are the 

which increases short-term variation in the lower primary type of off-channel habitat within this 

portions of the pool. In the Unimpounded Reach, reach and rehabilitation of side channels, or 

the narrower channel also increases short-term creation of new channels within old dike fi elds, 

variation in water levels because any change will be critical to increasing habitat diversity. 

in discharge through the constricted channel Strategies for reducing short-term variation in 

produces a proportionally larger change in water water levels within this reach are limited; thus, 

elevation compared to a wider channel. side channel rehabilitation will likely focus on 

ways maintain a connection to the main channel, Future Pressures and to maintain acceptable conditions of fl ow 

Any long-term change in discharge will also and water depths at some location within side affect mean water elevations. However, other channels, at different river discharges. factors and management decisions are likely to 

have more immediate effects. In the impounded Authors 

reaches, experiments using modifi ed procedures Robert Gaugush and Barry Johnson.

for dam operations and channel dredging have 

29
2.3 Water Quality Indicators Excessive nutrients can cause a range of 

problems in aquatic systems (Smith et al. 1999). Water quality indicators relate mainly to the One effect of high nutrient concentrations concentrations of important constituents in the is high rates of production. These high rates of water column. Nutrients and dissolved oxygen production produce a large amount of organic are critical elements in the survival and growth material that causes low oxygen concentrations of aquatic organisms, but high nutrient levels as it decomposes. A second effect of high algal can cause excessive plant growth. Chlorophyll a abundance is that light does not penetrate deeply is a common pigment in phytoplankton, tiny into the water and this can have a negative effect plants that live suspended in the water and form on the abundance and distribution of submersed 

the base of many aquatic food chains. Thus, the aquatic vegetation. High nutrient concentrations concentration of chlorophyll a is a measure of can also promote the occurrence of abundant phytoplankton abundance. Suspended solids are fi lamentous algae, which can have detrimental a measure of the amount of material suspended effects on submersed vegetation. In addition, in the water, which includes both soil particles high nutrient concentrations may also promote and biological materials. High concentrations rapid growth of duckweed, a small aquatic plant of suspended solids, whether due to high that fl oats on the surface. When duckweed is 

phytoplankton abundance or high silt loads, abundant, little light penetrates into the river. reduce light availability, which can reduce This may reduce submersed vegetation and growth of rooted aquatic plants. An indicator of promote conditions of low dissolved oxygen. In suitable winter habitat for fi shes in backwaters summary, excessive nutrients can lead to reduced uses a combination of temperature, dissolved submersed vegetation and dissolved oxygen oxygen concentrations, and water depth. The through a variety of mechanisms. Because right combination of these three factors produces vegetation is important as fi sh habitat and as food 

optimal conditions for fi sh survival in backwaters for waterfowl, excess nutrient concentrations during winter. may lead to less favorable habitats for fi sh and 

2.3.1 Major Nutrients (Total Nitrogen and Total waterfowl.

Phosphorus) High rates of algal production caused by high 

nutrient inputs can also cause problems when 

Assessment rivers are used as a drinking water source. Algal 

blooms can lead to taste and odor problems and Status: Fair in the upper reach, and fair to increase the frequency with which intake fi lters poor in the lower reaches and Illinois River. In need to be cleaned (Descy 1992). In addition to the Upper Impounded Reach (three upper pools) the impacts of nutrient inputs on algal production total nitrogen concentrations exceeded suggested in the river, delivery of excess nutrients to the guidelines about 50% of the time. In Pool 26, Gulf of Mexico by the Mississippi River causes the Open River Reach, and La Grange Pool, widespread hypoxia (low oxygen concentrations) total nitrogen concentrations exceeded suggested resulting in an extensive “dead zone” in the areas guidelines most of the time. Total phosphorus of the Gulf that receive nutrient input from the concentrations almost always exceeded suggested Mississippi River (Rabalais et al. 2002). guidelines in all LTRMP study areas.

Trend: Stable in all reaches. State of the Ecosystem

Purpose Total nitrogen (TN) concentrations in the 

main channel have increased substantially in Nitrogen and phosphorus are essential plant the UMR in the last century because of the nutrients required for the growth of algae and emergence of agriculture as the dominant aquatic plants. Nutrient inputs from sewage land use and associated high rates of fertilizer effl uent and urban and agricultural runoff can application, and increased urban inputs. In the result in excessive nutrient concentrations. 

early 1900s, TN concentrations in the UMR 

30
near Grafton (near the southern end of the changes in the types of crops grown, fertilizer 

Illinois River) were approximately 1.8 mg/L use, drainage systems, or land management 

(Goolsby and Battaglin 2001). From 1994 to may modify the input of nutrients from fi elds to 

2002, concentrations in the UMRS ranged waterways. 

from approximately 1 to 8 mg/L (Figure 2.3). The last 200 years of changes in agricultural 

Currently, the suggested range for TN land management and more recently in fertilizer 

concentrations for the UMRS is 0.6–2.18 mg/L application have led to substantial increases in 

(USEPA 2000a; Smith et al. 2003). This range nutrient concentrations in the UMR (Turner and 

applies to aquatic life rather than human Rabalais 2003). The changes that have led to 

health. It is based on the USEPA recommended current conditions have accumulated over many 

procedure for using the upper quartile of the years and it is almost certain that any changes in 

nutrient concentrations for reference streams land use and management practices undertaken in 

(0.6 mg/L) and the lower quartile of sampled the future to reduce nutrient concentrations will 

streams (2.18 mg/L) to defi ne an appropriate require many years before the effects of those 

range. We applied this procedure to data from the changes are fully realized (Turner and Rabalais 

“Corn Belt and Northern Great Plains” region 2003). 

(Smith et al. 2003), which encompassed several It is possible that some changes in 

of the sampled reaches. The three northern study management of river fl ows and fl oodplains 

reaches exceeded the suggested guidelines about could reduce overall nutrient export from the 

50% of the time, including at least one season— UMRS to the Gulf of Mexico. Backwater areas 

usually spring or summer—in every year from are locations of high rates of denitrifi cation, an 

1994 to 2002. The three southern reaches important nitrogen removal process (Richardson 

exceeded these guidelines most of the time. In et al. 2004; Strauss et al. 2004). Increasing 

La Grange Pool, mean TN concentrations were the fl ow of river water through backwaters or 

always greater than the guidelines. There were no restoring additional wetlands, particularly where 

signifi cant trends in TN concentration from 1994 tributaries join the river, may reduce nitrogen 

to 2002. transport in the UMRS. Management to increase 

For total phosphorus (TP), the suggested plant growth, such as summer water level 

guidelines are 0.01–0.08 mg/L as derived from reductions, can also reduce nutrient transport 

the procedures described above for TN (USEPA by storing nutrients in plant tissue, at least 

2000a; Smith et al. 2003). Concentration of TP temporarily. However, the overall magnitude of 

in the UMRS ranged from 0.05 to 0.3 mg/L nutrient reduction that can be achieved by such 

(Figure 2.4).and almost always exceeded the modifi cations of river hydrology and habitats is 

guidelines. There were no signifi cant trends in TP unknown.

from 1994 to 2002 for any study reach. Author

Future Pressures Jeffrey Houser.

Future changes in nutrient inputs to the river 2.3.2 Chlorophyll a are diffi cult to predict. Nutrient inputs are largely 

a function of outputs from sewage treatment Assessment plant and runoff from fertilizer applications 

on land. Increased human populations along Status: Mixed. In all locations chlorophyll 

the river would likely increase nutrient inputs. concentrations vary from low to high among 

Improvements in treatment of sewage and urban years and seasons. 

runoff would be needed to counteract the effects Trend: Stable in all reaches.

of increased population. In many parts of the Purpose

basin most of the land is already in agricultural Chlorophyll a concentration is a basic 

production so the land area used for agriculture measure of the abundance of suspended algae. is unlikely to increase substantially. However, These algae are an important part of the base of 

31
Figure 2.3. Total nitrogen (TN) concentrations in the main channel of the six Long Term Resource Monitoring Program study reaches 

from 1994 to 2002. Data points are means from stratifi ed random sampling episodes for winter, spring, summer, and fall. Error bars are 

one standard error. Dashed lines are lower and upper limits of suggested range for TN concentrations (USEPA 2000a; Smith et al. 2003). 

There are no signifi cant trends in TN for the period 1994–2002. 

32
Figure 2.4. Total phosphorus (TP) concentrations in the main channel stratum of the six Long Term Resource Monitoring Program study 

reaches from 1994 to 2002. Data points are means from stratifi ed random sampling episodes for winter, spring, summer, and fall. Error 

bars are one standard error. Dashed lines are lower and upper limits of suggested range for TP concentrations (USEPA 2000a; Smith et al. 

2003). There are no signifi cant trends in TP for the period 1994–2002.

33
the river food web, but excessive algal abundance velocity, and algal production in large rivers are 

can have negative effects on the river ecosystem. not well understood. Grazing by invasive Asian 

For example, high algal concentrations can carps (see section 2.8.7) and zebra mussels, 

reduce light penetration into the water column, which feed mainly by fi ltering algae from the 

which reduces growth of aquatic vegetation; water, may reduce chlorophyll concentrations in 

can cause low oxygen conditions when algae the river as their populations increase. 

die and decay; can increase costs of treatment Author for drinking water supplies; and may reduce the Jeffrey Houser. appeal of the river for recreational uses, such as 

swimming and boating, because of its negative 2.3.3 Total Suspended Solids effect on river aesthetics (Smith et al. 1999). 

State of the Ecosystem Assessment

Among seasons, years, and pools, Status: Mixed, ranging from good in the 

chlorophyll concentrations in the main channel upper reaches to fair-poor in the lower reaches 

vary among what is considered low (<10 μg/L), and Illinois River. Lower Pool 4 and Pool 8 were 

medium (10–30 μg/L), and high (>30 μg/L; generally below the maximum recommended 

based on the criteria in Dodds et al. 1998). The concentration for total suspended solids of 

UMRS main channel concentrations are most 25 mg/L. Upper Pool 4 and Pool 13 exceeded 

often in the medium (mesotrophic) range. Main the recommended concentration more frequently. 

channel concentrations in the UMRS generally Pool 26, the Open River Reach, and La Grange 

range from near 0 to 70 μg/L (Figure 2.5). Pool almost always exceeded the recommended 

Generally, concentrations are lowest in winter. concentration.

High chlorophyll concentrations were observed Trend: Stable or improving in Upper 

in spring 1994 in Pools 13 and 26 and in fall Impounded Reach (three upper pools). Stable in 

1996 in Pool 8 and may be the result of an all other reaches.

algal bloom during the sampling period. In all Purpose

three southern study reaches, high chlorophyll Total suspended solids (TSS) are a measure concentrations, indicating eutrophic conditions, of the concentration of particles in the water were more common in 2000–2002 than during column and are frequently cited as a primary the 1990s, however signifi cant trends over the water quality concern in the river. The TSS period of 1994–2002 were not observed. In affects aquatic vegetation by reducing light the upper pools eutrophic conditions occurred penetration into the water (Barko et al. 1982, less often in 2000–2002 than in the 1990s. The 1986; UMRCC 2003), which may reduce plant reasons for these changes are unclear but they growth and the feeding effi ciency of visual do not appear to be associated with changes in predators (e.g., bluegill [Lepomis macrochirus] nutrients (Figures 2.3 and 2.4) or total suspended or bass; Simon 1999). In addition, sediment solids (Figure 2.6). particles adsorb, transport, and store nutrients 

Future Pressures and pollutants (e.g., metals and dissolved organic 

Chlorophyll concentrations in large rivers compounds) in aquatic systems (Welch et al. 

are generally determined by light availability 1998). 

(largely determined by total suspended sediment Recent recommendations for TSS in the 

concentrations; see section 2.3.3 below), UMRS suggest that concentrations <25 mg/L 

nutrient availability, and current velocity. (as a summer average) are needed to establish 

Chlorophyll concentrations may respond to desired levels of aquatic vegetation (UMRCC 

changes in nutrients and light availability, but 2003). The 25 mg/L criterion was based on 

even qualitative predictions of future chlorophyll sustaining tuber production of wild celery 

concentrations are diffi cult because the relations (Vallisneria americana Michx) in areas of 0.8 m 

between nutrients, light availability, current depth or less (UMRCC 2003). If the guidelines 

34
Figure 2.5. Chlorophyll a concentrations in the main channel stratum of the six Long Term Resource Monitoring Program study reaches 

from 1994 to 2002. Data points are means from stratifi ed random sampling episodes for winter, spring, summer, and fall. Error bars are 

one standard error. Dashed lines represent the upper and lower bounds of “medium” chlorophyll concentrations (mesotrophic conditions) 

as defi ned by Dodds et al. 1998. Points above both dashed lines indicate “high” concentrations of algae (eutrophic conditions). 

35
are exceeded, negative effects on wild celery historical sediment deposits in many tributaries 

and other vegetation may occur. However, this are substantial (Knox et al. 1975; Knox and 

criterion may be unrealistic in the Unimpounded Faulkner 1994); thus, even if these practices are 

Reach, where TSS have always been high due to implemented soon, inputs from tributaries will 

inputs from the Missouri River (Meade 1995). likely change slowly. In addition, resuspension 

A separate criterion for the Unimpounded Reach of sediments by barge traffi c (Johnson 1976), 

should be considered. recreational boating (Knight and Parchure 2004), 

wind-generated waves, and bottom feeding fi sh State of the Ecosystem may also contribute to high concentrations. Concentration of TSS generally increased Future trends in barge traffi c are uncertain, but radically from upstream to downstream. 

Concentrations ranged from about 5 mg/L recreational boating is likely to increase. to Some management actions are being as high as 400 mg/L.There was considerable undertaken that may help reduce TSS. seasonal variation with highest concentrations Construction of islands in large open water typically occurring in spring and lowest during areas can reduce wind fetch and resuspension winter especially in the northern reaches of sediments caused by wind generated waves. (Figure 2.6) probably due to low fl ows, reduced Islands can also shelter areas from fl ow creating sediment inputs from the frozen watershed, quiet water that allows sediments to settle out. and reduced sediment resuspension under These effects can reduce TSS and promote the ice. All pools exceeded the recommended increased plant growth locally, but the effect at concentration of 25 mg/L on some occasions. the pool-wide scale is uncertain. Reduction of Lake Pepin, a natural riverine lake in Pool 4, acts pool water levels during summer (drawdowns) is as a natural settling basin, which reduces TSS another management option that may reduce TSS substantially downstream (Figure 2.6). The TSS concentrations (Landwehr et al. 2005). These concentrations in upper Pool 4 typically ranged drawdowns expose bottom sediments allowing from 20–60 mg/L (except during winter), but in them to dry and consolidate, and also promote lower Pool 4 were reduced to about 5–15 mg/L. growth of both submersed and emergent plants. Lower Pool 4 and Pool 8 were generally below As plant beds develop during summer, they help the 25 mg/L recommendation, though in many to anchor sediments, especially along shorelines. years Pool 8 had at least one season with mean Plant beds can also help reduce wind fetch and TSS concentrations above this level. Upper wave energy. This reduces sediment resuspension Pool 4 and Pool 13 were similar and exceeded and increases sedimentation within plant beds, the recommended maximum concentration thus reducing TSS. more frequently. Further down river, inputs 

from sediment laden tributaries increase TSS. Author

The three southern study reaches almost always Jeffrey Houser.

exceeded the recommended concentration. From 

2.3.4 Dissolved Oxygen 1994 to 2002, there was a signifi cant decline in 

TSS during fall in Pools 4 and 8, but no trends in Assessment other locations.

Status: Generally good, but with occasional Future Pressures episodes of low oxygen (hypoxia) in the upper 

High inputs of TSS from tributaries draining reaches. Winter hypoxia in the backwaters is 

catchments dominated by agriculture are a much more common in the Upper Impounded 

major source of TSS in the river (Wasley 2000). Reach than in Pool 26 or La Grange Pool. 

Changes in the types of crops grown or in land Trend: Stable. 

management may modify sediment inputs to Purpose waterways. “Best Management Practices” are 

often prescribed for uplands with a goal of Suffi cient dissolved oxygen (DO) 

reducing sediment runoff into streams. However, concentration is an important characteristic 

36
Figure 2.6. Total suspended solids (TSS) concentrations in the main channel stratum of the six Long Term Resource Monitoring Program 

study reaches from 1994 to 2002. Data points are means from stratifi ed random sampling episodes for winter, spring, summer, and fall. 

Error bars are one standard error. In Pool 4, data are shown for the upper and lower portions of the pool. These represent areas above and 

below Lake Pepin, a large, natural lake within the pool that acts as a settling basin. For 1994–2002 there was a signifi cant decreasing 

trend in TSS in Pools 4 and 8, with no trends in other locations. The horizontal dashed red line represents 25 mg/L, the recommended 

maximum summer mean concentration of TSS to establish rooted aquatic vegetation (Upper Mississippi River Conservation Committee 

Water Quality Technical Section 2003). The solid blue lines for Pools 4 and 8 represents the trend in fall TSS concentrations, with 90% 

confi dence intervals (dashed blue lines). Note that the scale of the vertical axis is much larger for Pool 26, Open River, and La Grange Pool 

(0–400 mg/L) than for the upper three pools (0–130 mg/L). 

37
of habitat suitability for aquatic organisms. 

The DO is determined by the balance between 

oxygen production by aquatic vegetation and 

algae and oxygen consumption by plant and 

animal respiration and decomposition of organic 

material. Excessive nutrient inputs that lead to 

excessive vegetation and algal production result 

in abundant organic material that can reduce DO 

concentrations to low levels as it is decomposed. 

The concentration of DO required varies among 

organisms, but 5 mg/L is used as a water quality 

standard by all of the UMRS states (Upper 

Mississippi River Basin Association 2004). 

In winter, mobility of some fi sh is limited by 

temperature so low current velocity environments with adequate DO concentrations are 

required. As a result, dissolved oxygen concentrations in backwaters during winter are of 

particular concern.

State of the Ecosystem

The DO data presented here were generally 

collected between mid-morning and midafternoon. Because minimum DO concentration 

typically occurs just before dawn, these data 

underestimate the true occurrence of low oxygen 

conditions. Nonetheless, the data provide 

important information on when and where 

low dissolved oxygen is likely to occur and 

indicate areas where these conditions are present 

throughout the day. 

Low oxygen conditions are more common 

in backwaters where water is slow moving and 

rates of oxygen consumption are high. The main 

channel is generally well mixed and oxygen 

consumption is relatively low; thus, oxygen 

concentrations are generally usually above 

5 mg/L. However, low oxygen concentrations 

have occurred in the main channel of La Grange 

Pool on the Illinois River (Table 2.2). Compared 

to the Mississippi River, the Illinois River has a 

lower gradient so the water moves more slowly 

and a higher load of organic material, which uses 

substantial oxygen during decomposition. 

Analysis of DO concentrations indicates 

that during winter 10% to 14% of the backwater 

area in Pools 4, 8, and 13 have mid-day DO 

concentrations below 5 mg/L and, during 

summer, 12–21% of the backwater area of 

Pools 8, 13, and 26 have DO concentrations less 

the 5 mg/L (Table 2.2; Fischer et al. 2005). In 

the upper three pools, the proportion of sampled 

backwater sites with low oxygen during winter is 

highly variable among years ranging from near 

zero to almost 40%. There were no trends during 

1994–2002 (Figure 2.7). In winter, snow on top 

of ice decreases light penetration and reduces the 

production of oxygen through photosynthesis by 

plants; thus, the depth of snow cover can be a 

useful predictor of the extent of winter hypoxia 

in backwaters of the upper pools (Fischer et 

al. 2005). In the lower pools, backwater winter 

hypoxia is rare. This is most likely a result of 

the minimal ice cover in these reaches and low 

winter water temperatures that increase the 

solubility of oxygen in water and reduce bacterial 

respiration and therefore oxygen demand. 

Future Pressures

The UMRS has probably always been a 

system with abundant organic material and 

may have always experienced some degree of 

winter hypoxia. Increased inputs of nutrients and 

organic materials, and reduced water volume 

in backwaters as they become shallower due 

Table 2.2. Mean percentage of stratifi ed random sampling 

sites with surface dissolved oxygen concentration <5 mg/L in 

winter and summer from 1993 to 2001. 

Strata

Study reach Main channel Backwater

Winter

Pool 4 0.4 (1.3)a 14 (14)b

Pool 8 0 13 (9)b

Pool 13 0 10 (5)b

Pool 26 0 6 (2)

Open River 0 --c

La Grange Pool 0 0.9 (3)

Summer

Pool 4 0.8 (3) 0.058 (0.07)

Pool 8 0.8 (2) 12 (8)b

Pool 13 0.3 (1) 21 (14)b

Pool 26 1.4 (4) 13 (10)b

Open River 1.3 (4) --c

La Grange Pool 25 (24)b 6.7 (6.7)

a

One standard deviation is shown in parentheses. 

b

Bold font indicates locations where the occurrence of 

low dissolved oxygen is >10% (modifi ed from Fischer et 

al. 2005).

c

There is no backwater strata in Open River Reach.

38
Figure 2.7. The percentage of backwater sampling sites where dissolved oxygen (DO) concentrations during winter, at the surface 

or just below ice cover, were <5 mg/L (1994–2002) for fi ve study reaches of the Long Term Resource Monitoring Program (there are no 

backwater sampling areas in Open River Reach). There were no signifi cant trends over the period 1994–2002.

39
to sedimentation, will likely increase hypoxia. almost no suitable habitat and percentage of 

In addition, many modifi cations to the main suitable habitat never exceeded 20% in Pools 

channel to facilitate navigation have resulted in 4 and 8. The estimated area of suitable habitat 

less water fl owing to backwaters to replenish was <10 ha in a few years for Pools 8 and 13, but 

oxygen supplies; thus, most management actions never <100 ha in Pool 26 and La Grange Pool. 

designed to increase oxygen concentrations Suitable habitat in Pool 4 area was below 50 ha 

focus on adjusting fl ow rates through backwaters in a few years during the 9-year period. 

during winter. The goal of this approach is to Of the three suitability criteria, low water 

provide fl ows that are high enough to maintain temperature is the most common cause of 

suffi cient dissolved oxygen concentrations but unsuitable winter conditions (Figure 2.9), 

low enough to maintain suitable habitat for followed by depth and dissolved oxygen. Shallow 

sport fi shes, such as bluegills. Reduced inputs of water depths also contribute to the problem, but 

nutrients and organic materials and increasing low dissolved oxygen concentration does not 

depth of backwaters by dredging may make it typically cause unsuitability in the UMRS. This 

easier to achieve habitat with both suitable DO combination of habitat characteristics is largely 

and current velocity. a function of water exchange between channels, 

where water is cold but with high oxygen Author levels, and backwaters, where water is slightly Jeffrey Houser. warmer but may have low oxygen. The rate of 

 2.3.5 Suitable winter habitat for sunfi shes in water exchange is affected by levees (natural or 

backwaters human-made) between channels and backwaters, 

the degree of water level fl uctuations during 

Assessment winter, and the water volume in backwaters. Data 

indicate that backwaters in Pools 4, 8, and 13 are Status: Poor in upper reaches, good in lower more likely to have lower water temperatures pools. There was relatively little suitable winter than more southern reaches. This may be due habitat in the upper reaches, but abundant winter to slightly lower water temperatures typically habitat in Pool 26 and La Grange Pool. found in the northern reaches during winter or to Trend: Stable.

differences in rates of water exchange between 

the main channel and backwaters. 

Purpose Despite relatively little suitable winter habitat 

Winter habitat conditions may cause in the northern reaches, the most common sunfi sh 

stress, or even mortality, for fi shes in rivers and bluegills (see section 2.8.1) are abundant 

(Johnson and Charlton 1960; Bodensteiner and in the upper pools. Thus, the usefulness of this 

Lewis 1992; Sheehan et al. 2004). Research metric as an indicator is questionable. Obviously 

has identifi ed suitable winter conditions for fi sh must survive through winter to maintain 

sunfi shes in backwaters as dissolved oxygen their populations, but we do not know how much 

concentration >5 mg/L, temperature >1.0o

 C, and suitable winter habitat is needed within a river 

depth >0.33 m of water (under ice). The LTRMP reach, nor how well fi sh survive in areas that do 

monitoring design can track these variables and not meet the suitability criteria. Suitable winter 

measure changes in the amount of suitable winter habitat is relatively rare in many river systems 

habitat through time. (Cunjak 1996), but suitable areas often support 

high densities of fi sh during winter (Carlson State of the Ecosystem 1992; Raibley et al. 1997). More investigation In the UMRS, only a small percentage of is needed of the effect of winter habitat the total backwater area sampled meets winter suitability compared to other factors affecting the habitat suitability criteria in the upper pools, abundance of sunfi shes. but percentages are much higher in lower pools 

(Figure 2.8). Pools 4, 8, and 13 have years with 

40
Figure 2.8. Percent of backwaters that contained suitable habitat for sunfi shes during winter from 1994 to 2002 based on a 

combination of temperature, dissolved oxygen, and depth in study reaches of the Long Term Resource Monitoring Program that have 

backwater habitats.

41
42

Figure 2.9. Mean percentage of backwater with suitable 

conditions during winter from 1994 and 2002 for temperature, 

dissolved oxygen (DO), and depth in study reaches of the Long 

Term Resource Monitoring Program that have backwater habitats. 

Future Pressures

Continued loss of natural levees and 

decreased volume in backwaters due to 

sedimentation means that winter habitat 

suitability will likely remain low in upper 

pools. Stabilizing water levels in the winter 

would reduce exchange rates and thereby 

increase water temperatures, but stable levels 

may reduce dissolved oxygen concentrations. 

Habitat construction projects aimed at increasing 

suitable winter habitat in backwaters must fi nd 

the right level of water exchange rates to assure 

a balance between suitable temperature and 

dissolved oxygen conditions; achieving that 

balance requires consideration of the geomorphic 

factors unique to each project area. Projects 

that increase depth in backwaters should result 

in more suitable habitat, until the deep areas 

fi ll with sediment again. Whether the level of 

suitability observed in the upper pools will have 

negative effects on the backwater fi sh community 

is unknown. However, projects designed to 

improve winter habitat may also have positive 

effects at other times of year and thus improve 

fi sh populations. 

Authors

James Rogala and James Fischer.
2.4 Sedimentation Indicators 2.4.1 Depth diversity in upper impounded areas

Sediments and sediment transport are Assessment 

integral parts of any large river. The processes Status: Poor. Above Pool 14 the processes of movement, storage, and resuspension of of sedimentation and erosion have reduced sediments produce the basic landscape mosaic depth diversity in the impounded areas since within the river channel and fl oodplain. construction of the dams. Conditions in pools But, over time, soil erosion from converting below 14, Open River Reach, and the Illinois prairies and forests to agriculture and urban River were not measured. areas has increased sediment fl ow in the river. Trend: Slightly degrading. Impoundments, such as dams, slow the fl ow 

and, often, more silt and sand are delivered Purpose

than can be moved by the river. The resulting Diversity is a positive attribute of healthy, 

sediment accumulation can reduce habitat for natural systems. Water depth is a critical feature 

plants, invertebrates, and fi sh; degrade water of rivers defi ning habitat suitability for many 

quality; and restrict opportunities for recreational biota. Other habitat components, such as water 

boating. Changes to water depth as a result velocity, are correlated to water depth. Therefore, 

of sedimentation are refl ected in the indicator diversity in water depth should produce diversity 

of depth diversity in impounded areas (the in vegetation, fi sh, and wildlife. Water depth 

large open water areas above dams) during the is a product of water elevation, which changes 

50 years from 1940, soon after impoundment, seasonally, and elevation of the river bottom 

to 1990. Sedimentation rates in backwaters and fl oodplain, which usually changes slowly. 

refl ect increased sediment infl ows over time and Changes in depth diversity over long periods 

changes in fl ow patterns implemented to support (more than about 20 years) can be detected by 

navigation. The indicator for net sedimentation repeated bathymetric surveys.

in backwaters captures changes in three locations State of the Ecosystem over a recent 5-year period. These indicators 

were measured only in Pools 4, 8, and 13, but Large open-water impounded areas were 

sedimentation is a continuing problem in most of formed in most of the pools above Pool 14 by 

the UMRS. construction of the dams in the late 1930s. In 

Both of these indicators are directly related impounded areas, water velocity slows, which 

to processes of sediment movements. Hydrology allows sediment to settle out, and wind produces 

and landscape modifi cations are important substantial waves, which erode shorelines and 

factors underlying these processes. There are resuspends sediments. During the fi rst 50 years 

management techniques that can be applied since impoundment, the combination of sediment 

to the uplands to reduce inputs of sediment to deposition in deep areas and erosion of shallow 

tributary streams and ultimately to the UMRS. areas resulted in a extensive loss of depth 

However, due to the substantial amounts of diversity in these impounded areas (Figure 2.10). 

sediment already stored in tributaries, it may In a study area within the impounded area 

take many years before improvements in land of Pool 13, these two processes seem to be 

management results in substantial reductions of converging to produce a uniform depth of about 

sediment inputs to the Mississippi and Illinois 1.2 m. 

Rivers. There are also a variety of techniques A comparison of lower resolution data 

that managers have applied to river channels from the 1930s for Pools 4, 8, and 13 shows 

and fl oodplains that can have locally positive similar change over the same 50-year period 

effects on sediment dynamics (both erosion and (Figure 2.10). To quantify changes in diversity, 

deposition) and on habitats. we compared total length of the contour lines in 

the impounded areas between 1940 and 1990. 

Over the 50-year period, Pool 4 showed a 25% 

43
Figure 2.10. Change in water depths for the impounded areas in Pools 4, 8, and 13 of the Upper Mississippi River from 1940 to 1990. 

Water depth intervals are 1.5 meters, with dark colors depicting deeper areas.

44
loss in depth diversity, Pool 8 a 49% loss, and 2.4.2 Net Sedimentation Rates in Backwaters of 

Pool 13 a 47% loss. These numbers are likely the Upper Impounded Reach

an under-estimate, as the recent database has a 

higher resolution; thus, ability to detect the edges Assessment

is greater. Status: Mixed. 

Though poorly documented in recent years, Trend: Overall degrading. Rates of sediment 

it is expected the process of erosion in shallow accumulation are highly variable in space and 

areas and deposition in deeper areas is ongoing. over short periods, but overall accumulation rates 

The rate of change has likely decreased as are still of concern. Conditions in pools below 

shallow areas eroded and deep areas fi lled, 14 and the Illinois River were not measured. No 

but considerable island erosion has still been backwaters occur in the Open River Reach.

observed recently. Habitat improvements 

performed by the Environmental Management Purpose Program have countered the loss of diversity 

through island building and dredging projects. Accumulation of sediments in backwaters is 

a normal process in rivers. However, increased Future Pressures sediment inputs can speed up this accumulation 

The physical forces that cause loss of depth and reduce the amount of deep water habitat, 

diversity will not change in the future, but especially in areas with low fl ow. These changes 

the question of whether equilibrium between have consequences for many fi sh and wildlife 

erosion and deposition has been reached remains that rely on deep, off-channel areas during some 

unanswered. Repetitive surveys in the future will portion of their life history. Detecting change 

provide those answers. Given the substantial through repeated measurement of water depth at 

change that has occurred since impoundment, specifi c locations can provide good estimates of 

future changes should occur more slowly. change over short periods (5 years or less), but 

Rehabilitation projects can increase diversity high variability in the data makes detection of 

directly through island building and dredging. overall change diffi cult.

Islands are built using designs that are resistant State of the Ecosystem to erosion. In addition, islands reduce windgenerated wave action and both islands and Most pre-LTRMP studies found high 

dredging help to concentrate fl ows in deep areas; rates of sediment accumulation after dam 

thus, these projects modify the physical forces construction. However, many of these represent 

that cause loss of depth diversity. Restoring maximum rates in high deposition areas because 

low water levels in the summer (i.e., drawdown most studies did not average rates across all 

projects) may have mixed effects on depth backwaters. In addition, sedimentation rates 

diversity. Drawdowns can expose and consolidate have likely decreased over time due to reduced 

fi ne sediments with high organic content, sediment trapping effi ciency as backwaters 

which increases depth. These consolidated became shallower. LTRMP monitoring between 

sediments have less potential for resuspension 1997 and 2001 in backwaters of Pools 4, 8, 

and transport, thus minimizing erosion. But and 13 indicate that sedimentation rates were 

drawdowns may also increase erosion in tributary highly variable both within and among years 

deltas and in shallow aquatic areas. We will have (Figure 2.11). Rates were lower than measured 

a greater ability to detect future changes in water in most previous studies but generally increased 

depth diversity, as we now have high resolution from Pool 4 to Pool 13. 

maps of water depth from 1990 for many pools The work in Pools 4, 8, and 13 indicated 

of the UMRS. that rates of sediment accumulation and erosion 

were related to discharge and water depth or Author land elevation. At the time of the surveys, high 

 James Rogala. discharge (e.g., 2001, Figure 2.1) resulted in 

sediment deposition in terrestrial areas and 

45
Figure 2.11. Annual net sedimentation rates for aquatic areas (blue) and terrestrial areas (green) in backwaters of Pools 4, 8, and 13 

between 1997 and 2001. A negative sedimentation rate indicates that erosion was greater than sediment deposition in that year. Bars 

represent standard errors.

46
sediment erosion in aquatic areas. This relation are either created by deposition or removed 

with discharge was also refl ected along the through erosion. Replacing lost natural levees 

elevation gradient of transects, where deep with human-made structures will maintain 

areas accumulated sediments in low discharge present conditions. The future net gain or loss of 

years and were eroded in high discharge years. these protective barriers is unknown. Managers 

Changes in these relations between discharge are considering sediment transport in designing 

and sedimentation rates would indicate process habitat rehabilitation projects so that delivery of 

changes that may have effects across a wide sediments to backwaters can be reduced and the 

range of physical and biological components. occurrence of high-velocity fl ushing fl ows can be 

increased. Future changes in the relation between Future Pressures sedimentation, discharge, and water depth will be Sediment delivery to the UMR is not an indicator of changes in the overall process of expected to decline substantially in the near sedimentation.

future. The fate of these delivered suspended 

sediments will depend on sediment transport Author

effi ciency. Transport effi ciency will change as James Rogala.

natural levees protecting backwaters from fl ow 

47
2.5 Land Cover/Land Use Indicators Purpose

Floodplain forests are an important The pattern of land cover within a river’s component of large river ecosystems. They fl oodplain is the result of river dynamics and provide habitat for a broad range of plants and human intervention. Cities and farm fi elds behind 

animals and play an essential role in maintaining levees are obvious modifi cations, but changes the biological diversity of the UMRS. In in vegetation and habitat types can be the result addition, floodplain forests reduce soil erosion of more subtle changes in fl ows or water levels. 

and improve water quality by trapping sediment A healthy river fl oodplain consists of a diverse and sequestering plant nutrients. matrix of habitat types that are connected to the 

river by occasional fl ooding. This connection State of the Ecosystem

is critical to maintaining dynamic physical and Area of fl oodplain forest declined in 24 of 

chemical processes that support diverse plant and 31 reaches of the UMRS between 1989 and 

animal communities. 2000 with a system-wide decrease of 5%, or 

The emergent vegetation indicator tracks 17,000 acres (Figure 2.12). The greatest decline 

the amount of aquatic vegetation growing along was in Pool 18, where forest area decreased 

shorelines and in wetlands, which is affected by by 27% (4,700 acres). When considered by 

variation in water levels, both annually and daily. river reach, a decline of 3,400 acres (4%) in 

Changes in the amount of fl oodplain forest are fl oodplain forest coverage occurred in the Upper 

most indicative of changes in fl ooding regimes Impounded Reach (Pools 1–13), 11,600 acres 

and in ground water levels. The percentage of (9%) in the Lower Impounded Reach (Pools 

the fl oodplain behind levees indicates how much 14–26), and 3,200 acres (4%) in the Illinois River 

of the historical fl oodplain no longer receives pools. In contrast, there was a slight increase of 

periodic fl ooding and has therefore lost much of 1,200 acres (2%) in fl oodplain forest coverage in 

its ecological connection to the river. the Unimpounded Reach.

Data for these indicators were derived from Floodplain forests in the UMRS cover only 

land cover maps developed by the LTRMP for a small portion of the area that they did before 

1989 and 2000 that cover the entire river corridor European settlement (Nelson et al. 1994; Yin et 

of the UMRS. The graphics for these indicators al. 1997). Forest acreage decreased rapidly in are depicted within the four major reaches of the the nineteenth century as trees were harvested 

system and include data for Pools 1–26, the north and land was converted to agricultural and urban 

and south sections of the Unimpounded Reach, uses. Differences in fl oodplain forest coverage 

and for the Alton, La Grange, and Peoria Pools between 1989 and 2000 indicate that, although 

of the Illinois River. In the Unimpounded Reach, the rate has slowed, declines in fl oodplain forest 

the south section was from the mouth of the Ohio are still occurring in the UMRS. Changes due 

River north to river mile 80 near Grand Tower, to conversion to agriculture have slowed, but 

Illinois, and the north section covered river mile forests are still adjusting to ecological changes 80–230, just below Lock and Dam 26. associated with impoundment and water level 

changes. 2.5.1 Floodplain Forest Modifi ed processes within the fl oodplain can 

have negative effects on forests. Maintaining Assessment: 

high water elevations at low fl ows (see section Status: Mixed. 2.2.2) has increased the ground water elevation Trend: Degrading in impounded reaches, and caused a shift to trees that can tolerate stable in the Open River Reach. Between 1989 wetter conditions, mainly silver maple (Acer and 2000, area of fl oodplain forest declined in saccharinum). In addition, high short-term all reaches of the UMRS except for the Open variation in water levels (daily or weekly) and River Reach. Further declines are expected in high sedimentation rates on the fl oodplain in impounded reaches. Reforestation efforts in the some years have acted to reduce recruitment of Open River Reach may increase forested area. 

48
Figure 2.12. The area (acres) of fl oodplain forest in the Upper Mississippi River System based on 1989 and 2000 land cover 

maps produced by the Long Term Resource Monitoring Program. Data are presented for Pools 1–26, north and south sections of the 

Unimpounded Reach (border at river mile 80), and for the Alton, La Grange, and Peoria Pools of the Illinois River.

49

Mississippi River

Illinois River
many tree species. The Great Flood of 1993 was Purpose

an unusual event because fl ood waters did not Emergent vegetation describes a variety of 

recede until late summer, which killed many trees annual and perennial plants that grow in moist or 

in the southern reaches of the UMRS. Studies are seasonally fl ooded soils, along shorelines or in 

now under way to determine the extent of forest marshes. Typical plants include wild rice, cattail, 

regeneration in those areas and the effects on arrowhead, bulrushes, smartweed, and sedges. 

species composition in forest communities. Emergent plants are an important part of the 

Relating changes in forest acreage to other transition zone between terrestrial and open water 

river components is diffi cult. Whereas, water habitats and indicate a healthy hydrologic regime 

quality variables, such as total suspended solids, in fl oodplain rivers. They provide important food 

nutrient concentrations, and sedimentation rates and habitat resources for a wide variety of fi sh, 

are probably affected by decreases in fl oodplain amphibians, reptiles, birds, and mammals, help 

forest, these variables are infl uenced by a wide to prevent erosion by holding sediments in place 

variety of factors and our ability to isolate the along shorelines, and are indicators of the extent 

effect of fl oodplain forests based on monitoring of critical marsh habitats. 

data is limited. In addition, a 5% decline in State of the Ecosystem fl oodplain forest between 1989 and 2000 is 

relatively small and might not be expected to The percentage of total area in emergent 

produce detectable changes in water quality vegetation ranged from 0% to 10% among 

variables. different reaches of the UMRS and averaged 

about 5%. Emergent vegetation was most Future Pressures prevalent in the Upper Impounded Reach 

Historically, declines of fl oodplain forests (Figure 2.13). Between 1989 and 2000, coverage 

have occurred in response to agricultural of emergent vegetation generally decreased by 

conversion and urban development. These about 5,000 acres in the Upper Impounded Reach 

pressures are likely to continue, but at slower (Pools 1–13), but increased in all other reaches. 

rates. The effects of impoundment and of Changes were most noteworthy in the Illinois 

changes in water regime will continue to affect River pools (total increase of about 7,500 acres), 

the survival and reproduction of forest trees. but the areal extent of emergent vegetation was 

These effects may result in changes in the species still relatively small at 1% in Alton Pool, 4% in 

composition of forests or in conversion of forests La Grange Pool, and 3% in Peoria Pool. No goals 

to other vegetation types. Reforestation efforts for abundance of emergent vegetation have been 

can have positive effects locally, but large scale established in the UMRS. 

effects will likely require changes in underlying Abundance of emergent vegetation is 

ecological conditions. subject to considerable seasonal and annual 

Authors variation and is highly dependent on water level 

fl uctuations. Drought conditions preceding the Kirk Lohman, Larry Robinson, and John 1989 mapping may have infl uenced the extent of Nelson.

emergent vegetation and a recovery from those 

2.5.2 Emergent Vegetation conditions in the lower reaches may be refl ected 

in the 2000 coverage. Increases in the Illinois 

Assessment: River pools may be the result of more favorable 

Status: Fair to good. Emergent vegetation is water regimes for a few years before 2000, as 

most abundant in the Upper Impounded Reach. well as management actions, such as planting, to 

Trend: Mixed. Emergent vegetation has promote the growth of emergent vegetation. 

decreased in the Upper Impounded Reach and Future Pressures

increased in all other reaches. Abundance of emergent vegetation is highly 

affected by water levels. Emergent plants have 

evolved to take advantage of the predictable 

50
Figure 2.13. The area of emergent vegetation (acres of deep and shallow marsh combined) in the Upper Mississippi River System 

based on 1989 and 2000 land cover maps produced by the Long Term Resource Monitoring Program. Data are presented for Pools 1–26, 

north and south sections of the Unimpounded Reach (border at river mile 80), and for the Alton, La Grange, and Peoria Pools of the Illinois 

River. 

51

Mississippi River

Illinois River
annual cycle of high and low water levels that are used by many animals for at least part of their life 

part of a healthy large river. In the UMRS, the cycle. In addition, fl oodplains act as buffers that 

dams hold water levels artifi cially high during store fl oodwaters then release them slowly, which 

low fl ows to promote commercial navigation. reduces fl ood heights and subsequent damage to 

In some navigation pools, dam operations result human-made structures in the fl oodplain. 

in large, short-term fl uctuations in water levels. However, fl oodplains are also highly valued 

Both are stressors for emergent vegetation, but by humans because they provide fertile, fl at 

both can be managed for a better ecological lands for agriculture and urban development, 

response. Recent management actions to reduce and provide direct access to the river for 

water levels during summer (drawdowns) have transportation and recreation. To maximize the 

been successful at increasing the abundance of value of fl oodplains for human use, landowners 

emergent plants at locations in both the Upper often build levees that keep fl oodwaters out. 

and Lower Impounded Reaches. Changes in This has obvious benefi ts to landowners who can 

dam operations to reduce short-term variation increase the direct economic returns from their 

in water levels are being explored. In addition, property. But, levees also constrict the fl oodplain 

habitat rehabilitation projects, such as island and reduce storage of fl oodwater, which increases 

building and fl ow modifi cations, can promote fl ood heights near and upstream of the levee. 

local conditions to increase growth of emergent In addition, levees eliminate the connection of 

vegetation and provide needed habitat and food the river to its fl oodplain, which has negative 

resources in strategic locations. effects on the ecological processes and services 

mentioned above. Authors The data for this indicator were derived 

Kirk Lohman, Larry Robinson, and John by applying a Geographic Information System Nelson. coverage of levee locations developed by 

2.5.3 Area of Floodplain Behind Levees the Scientifi c Assessment and Strategy Team 

(available at http://edc.usgs.gov/sast/) following 

Assessment: the fl ood of 1993 to land cover maps generated 

by the LTRMP for 2000. Because there was only Status: Mixed. The Upper Impounded one levee coverage map available, calculating Reach has almost no levees and connection to 

change over time was not possible. Thus, this the fl oodplain is good. The amount of leveed indicator shows status only. fl oodplain increases extensively in the lower 

reaches. State of the Ecosystem

Trend: No trends–Status only. This indicator The data show a distinct gradient of is based on a single coverage depicting UMRS increasing fl oodplain area sequestered behind levees in 1993; thus, calculation of change over levees from upper to lower reaches of the time was not possible. UMRS (Figure 2.14). The Upper Impounded 

Purpose Reach (Pools 1–13) has little leveed area (about 

4% total) and virtually the entire fl oodplain is The UMRS, like most large rivers, has a connected to the river. In the Lower Impounded fl oodplain that was historically subjected to Reach, the number of levees increases annual fl ooding. Floodwaters bring fresh supplies substantially and leveed area accounts for 48% of of nutrients, sediments, and organic matter to the total fl oodplain. In the Unimpounded Reach, terrestrial areas and off-channel water bodies, levees are prominent resulting in about 67% and sometimes scour and resculpt these areas. of fl oodplain area behind levees. In this reach, Active fl oodplains are subject to alternate wetting almost all of the active (frequently fl ooded) and drying of soils, which produces dynamic fl oodplain is in narrow strips of land between the chemical and physical conditions. Healthy river and levees known as batture lands. In the fl oodplains are highly productive, contain a wide Illinois River, the two lower pools are heavily variety of vegetation and habitat types, and are leveed (about 60% of total area), whereas the 

52
Figure 2.14. The percentage of the total fl oodplain area that was behind levees within the Upper Mississippi River System based on 

levee coverage developed by the Scientifi c Assessment and Strategy Team (available at http://edc.usgs.gov/sast/) then applied to the 

2000 land cover maps produced by the Long Term Resource Monitoring Program. Data are presented for Pools 1–26, north and south 

sections of the Unimpounded Reach (border at river mile 80), and for the Alton, La Grange, and Peoria Pools of the Illinois River. 

53

Mississippi River

Illinois River
Peoria Pool and areas above have few levees. Future Pressures

Total across all three reaches on the Illinois is It is unlikely that many new levees will be 

about 50%. built in the UMRS, although some expansion 

Most of the levees on the system protect land is still occurring in urban areas (Pinter 2005b). 

used for agriculture or urban areas, but a few are Most existing levees are likely to be maintained 

managed by resource management agencies or for the foreseeable future, but some may revert 

hunting clubs as moist soil units for waterfowl to public ownership if both funds and willing 

habitat or for other recreational purposes. A few sellers are available. Management of reverted 

levee districts have been purchased by agencies levee districts will probably involve some 

or environmental organizations and are being reconnection to river fl ows, either through 

rehabilitated for ecological benefi ts. Most of permanent breeching of levees or using gates to 

these rehabilitation plans involve some type of control water exchange for specifi c management 

levee breeching and periodic refl ooding of these objectives. However, conversions of leveed areas 

lands. Examples are the Emiquon and Spunky to public land are expected to be slow and large 

Bottoms projects on the Illinois River fl oodplain. changes in this indicator are not expected in the 

These former levee districts are now being near term. 

restored by a partnership of agencies headed by An alternative to public ownership of 

The Nature Conservancy (see http://www.nature. fl oodplains is to develop new uses for fl oodplain 

org/wherewework/northamerica/states/illinois/ lands that are compatible with occasional 

press/emiquon.html). fl ooding (The Wetlands Initiative 1997). Such 

Specifi c targets for the percentage of active uses might allow landowners to remove levees 

(unleveed) fl oodplain required for a healthy river or to lower them allowing more frequent 

ecosystem do not exist. The amount of fl oodplain fl ooding of the protected lands. Potential new 

required to maintain critical ecosystem services, uses could involve growing crops that can 

such as waste assimilation, biotic diversity, and withstand occasional fl ooding, such as forest 

water supply, is unknown. In addition, we do trees, hay, or native wildfl owers and wetland 

not know if river channels should be managed plants, or developing private reserves for 

for different ecological responses in locations fee-based hunting and trapping. In addition, 

where connection to the fl oodplain is high agencies or municipalities could develop fee-

(the Upper Impounded Reach) compared to based easements with landowners to allow use 

locations with little fl oodplain connection (the of leveed areas for storage of fl oodwaters or 

Unimpounded Reach). Management experiments nutrients. 

and focused research are needed to determine 

Authors relations between fl ood frequency and ecological 

responses. However, any management targets for Kirk Lohman, Larry Robinson, and John 

amount of leveed fl oodplain are likely to differ Nelson.

among river reaches given the economic realities 

of current land ownership patterns. 

54
2.6 Aquatic Vegetation Indicators (Mills 1966; Bellrose et al. 1979). A massive dieout in the mid-1950s was one critical indicator 

Submersed aquatic vegetation consists of of ecological degradation of the Illinois River the larger plants found under, or fl oating on, (Sparks 1984). Growth of aquatic vegetation, the water. For these plants, light must penetrate including submersed, emergent, and fl oating-leaf the water to provide the sun energy needed to plants, was excellent in the Upper Impounded begin growth in spring and maintain it during pools with lesser amounts in lower pools the entire growing season. Thus, the distribution from the 1940s to early 1970s (Green 1984). and abundance of submersed vegetation depends Symptoms of deterioration became apparent after mainly on water depth (which changes with the late 1970s. A widespread and sudden decline water levels) and transparency (which depends of wild celery (Vallisneria americana) in the mainly on levels of suspended solids). In the late 1980s elevated the concern that the UMR 

Unimpounded Reach of the UMRS, these might be on the verge of major shift in vegetation conditions are poor and aquatic vegetation has conditions. Monitoring of submersed aquatic been virtually absent, thus the LTRMP did not vegetation was initiated in 1991 to establish sample for vegetation in the Open River Reach. a reference point of status and track future Submersed plants can be a food source for changes. The percentage frequency of occurrence animals, but also provide important physical of submersed aquatic vegetation (all species structure for invertebrates and fi sh. Many of the combined) is used as the primary indicator of management actions implemented on the river the status of submersed aquatic vegetation in the include a goal of restoring submersed vegetation. system (Rogers et al. 1998; Yin et al. 2000). Sampling for submersed aquatic vegetation 

by the LTRMP began in 1991 using fi xed State of the Ecosystem

transects in selected backwaters of Pools 4, 8, The distribution of submersed aquatic 

and 13. In 1998, stratifi ed random sampling vegetation in the UMR displayed a distinct 

was added in these pools and in Pool 26 and longitudinal pattern. Submersed aquatic 

La Grange Pool on the Illinois River. After vegetation was common in shallow backwaters 

3 years of conducting both types of sampling, in the Upper Impounded Reach (Figure 2.15), 

transect sampling was discontinued in 2000. Data but was seldom detected in Pool 26 or the Illinois 

from both sampling designs are included for this River. Besides annual sampling in LTRMP 

indicator. reaches, additional sampling conducted in 

other locations for research studies indicated 

2.6.1 Submersed Aquatic Vegetation that submersed vegetation decreased rapidly 

below Lock and Dam 13 and rarely occurred Assessment downstream of Lock and Dam 19 or in the 

Status: Mixed. Generally good in the Illinois River. Aquatic vegetation was historically Upper Impounded Reach, poor in Pool 26 and absent from the Open River Reach due to lack La Grange Pool where aquatic vegetation rarely of appropriate habitat; thus, sampling was not 

occurs. conducted in that reach. 

Trend: Stable, but with a decreasing trend in The LTRMP data revealed that submersed 

the upper portions of Pool 4. Fluctuates annually aquatic vegetation in upper Pool 4 (upstream of in the Upper Impounded Reach depending on Lake Pepin) has declined steadily since 1991. water levels and water clarity. Specifi c reasons for the decline are unknown but 

Purpose may be associated with relatively high levels of 

nutrients and turbidity associated with inputs Submersed aquatic vegetation provides an from the Minneapolis/St. Paul metropolitan important food source for migratory waterfowl area and from the Minnesota River. Lake Pepin and habitat for fi sh. The Illinois River harbored 

acts as settling basin; thus, water downstream abundant aquatic vegetation in its expansive is clearer and more conducive to growing backwaters until the early twentieth century 

55
56

Figure 2.15. Percent frequency of occurrence of submersed aquatic vegetation in the Long Term Resource Monitoring Program sampling 

pools from 1991 to 2004. Spring (green lines) and summer (blue lines) transect sampling was conducted in selected backwaters from 

1991 to 2000. Stratifi ed random sampling (black lines) was conducted in all shallow water areas (<2.5 m) connected to the river channel 

beginning in 1998. The gray lines in the graph for upper Pool 4 indicate a signifi cant decreasing trend in vegetation abundance in spring 

with 90% confi dence intervals. 
submersed vegetation. Lower Pool 4, Pool 8, and for drawdowns in the Lower Impounded Reach 

Pool 13 experienced fl uctuations in submersed (Pools 24, 25, and 26), response of submersed 

vegetation, but appeared to be highly resilient. vegetation was limited due to high turbidity.

Frequency of occurrence of submersed aquatic Future Pressures vegetation in Pool 26 of the Upper Mississippi Although upper Pool 4 is only a small River and La Grange Pool of the Illinois River section of the key monitoring reaches, the was limited. Occasionally, small increases in rapid decrease of submersed aquatic vegetation submersed vegetation occurred immediately over 12 years demonstrates the fragility of the following lower water levels, but these seldom UMR ecosystem. Focused research is needed persisted. to identify environmental factors that caused It appears that low water clarity and short- the progressive degradation so that effective term variation in water levels are the primary measures can be taken to prevent declining trends factors limiting distribution of submersed over larger areas. vegetation (Yin and Langrehr 2005). Both factors Low water clarity and high variability in are especially evident below Pool 13 and are water levels are expected to persist below Lock probably the main factors responsible for the and Dam 13. Habitat enhancement projects, reduced occurrence of submersed vegetation such as island construction, may create protected in lower reaches. Recent experiments with areas where sediments can settle out and increase summer water level reductions (drawdowns) water clarity enough to allow plant growth. in the impounded reaches have shown mixed Both summer drawdowns and changes in dam responses for submersed vegetation. In the operations that reduce short-term water level Upper Impounded Reach, drawdowns typically variation can enhance conditions for submersed increased occurrence of submersed vegetation vegetation in shallow areas. in areas where water depth had been limiting, 

but decreased occurrence in shallow areas where Author

emergent vegetation was reestablished. However, Yao Yin.

57
2.7 Macroinvertebrate Indicators State of the Ecosystem

Macroinvertebrates are the small animals that In the 1950s, much concern arose when 

mayfl y densities dropped extensively in the live in the river bottom or on plants and logs in UMRS and in Lake Erie (Fremling 1964; Mills the water. These organisms are important food et al. 1966; Kreiger et al. 1996). Low dissolved sources for many fish, shorebirds, and ducks. oxygen levels due to pollution were thought And, because they live on the bottom, they to be the cause. In 1926, the Mississippi River can be good indicators of healthy conditions in from St. Paul to Lock and Dam 3 had dissolved river sediments. However, macroinvertebrate oxygen levels <1 mg/L. By 1987, dissolved abundance is usually highly variable in oxygen levels had rebounded to 7 mg/L or rivers, even when populations are healthy. greater following substantial reductions in Thus, ascribing changes in abundance to any pollutants (Johnston and Aasen 1989) and specifi c driver can be diffi cult. Data on the 

increased abundance of mayfl ies was detected in abundance of mayfl ies and fi ngernail clams Pools 2 and 4 (Fremling 1989). Dynamic year- (Musculium transversum) is indicative of the to-year variation in mayfl y abundance was also amount and quality of soft sediment habitats reported in Pool 19 (Carlander et al. 1967) where and water quality within the river. Sampling for estimated pool populations ranged from 3.6 invertebrates under the LTRMP was discontinued 

billion in 1959 to 23.6 billion in 1962. after 2004 due to budget considerations. The LTRMP data show large differences 

2.7.1 Burrowing Mayfl ies in mayfl y abundances among the study areas. 

Mayfl y densities were relatively high (50 to 

Assessment 250 per square meter) in the upper pools of the 

Status: Mixed. Burrowing mayfl ies UMRS (Pools 4, 8, and 13; Figure 2.16), but 

(Hexagenia spp.) were relatively abundant in the consistently lower (generally <25/m2

) in Pool 

Upper Impounded Reach but with much lower 26, La Grange Pool, and the Open River Reach. 

abundance in Pool 26, the Open River Reach, There were no trends in mayfl y abundance 

and La Grange Pool. between 1993 and 2004. 

Trend: Stable, but with considerable annual The mixed systemic status of mayfl ies 

variation. suggests that environmental conditions are 

better in the upper reaches of the river. Lower Purpose reaches have much lower mayfl y densities The main objective of the LTRMP (roughly a factor of 4), which may indicate macroinvertebrate component is to provide a a population under environmental stress or better understanding of the conditions needed that environmental conditions simply are not to support viable populations of benthic conducive to supporting the larger populations invertebrates that are important foods for native seen in the upper system. Historically, both Pool fi shes and migrating waterfowl. 26 and La Grange Pool have supported large A number of studies have shown that number of mayfl ies (Fremling 1964; Mills et burrowing mayfl ies are ecologically important al. 1966). Possible reasons for the differences as food for fi sh and waterfowl and as biological include differences in substrate type and quality, indicators (Hoopes 1960; Jude 1968; Ranthum chlorophyll levels, dissolved oxygen levels, 1969; Thompson 1973; Myslinski and Ginsburg discharge levels, or temperatures. The densities 1977; Kushlan 1978; Eldridge 1988; Rosenberg of mayfl ies reported by LTRMP are within the and Resh 1993; Steingraber and Weiner 1995; ranges reported in other studies (Sauer 2004). Tyson and Knight 2001). Mayfl y distribution and The fl uctuations indicate that mayfl ies are able 

abundance have been used as indicators of water to rebound if conditions are right even when quality on the UMRS (Fremling 1964; 1989; population levels are low, such as in the southern Johnston and Aasen 1989); thus, the abundance reaches. 

of mayfl ies is of great interest to managers. 

58
Figure 2.16. Estimated density of mayfl ies (Hexagenia spp; no/m2

 ±1 standard error) weighted by area of strata within each study area 

of the Long Term Resource Monitoring Program from 1993 to 2004. In Pools 4 and 26 and La Grange Pool, density of mayfl ies was not 

estimated in 2003. 

59
Future Pressures 1968; Ranthum 1969; Thompson 1973; Kushlan 

There is no current management objective for 1978; Eldridge 1988). Fingernail clams can 

mayfl y abundance in the UMRS. Other systems, also be sensitive to periods of low oxygen or 

such as the Great Lakes, have established high ammonia concentrations, conditions often 

indicators of ecosystem health for mayfl ies; associated with high temperatures, low fl ows, or 

however, abundance was used as an indicator of high levels of organic pollutants (Anderson et al. 

water and sediment quality, not as a measure of 1978; Sandusky and Sparks 1979; Sparks 1980). 

food availability. Although LTRMP data yield Thus, the abundance of fi ngernail clams is of 

adequate pool-wide mean estimates for the study great interest to managers. 

reaches, no other comprehensive inventories State of the Ecosystem

were made in the past, therefore direct historical Similar to mayfl ies, fi ngernail clams also comparisons are not possible. experience boom and bust cycles in abundance. Burrowing mayfl ies prefer soft, silty For example, Wilson et al. (1995) reported substrates that allow them to burrow and they that in 1985 fi ngernail clam densities averaged are sensitive to sediment type and quality as well 30,000/m2

 in Pool 19. By 1990, no fi ngernail as low oxygen levels resulting from nutrient clams were found, but recently densities have inputs and toxic pollutants in bottom sediments. rebounded to about 50,000/m2

 in Pool 19 (Rick Urban, agricultural, and stormwater runoff are Anderson, Western Illinois University, personal currently sources of these nutrient inputs and communication). Fingernail clam populations pollutants. Watershed and regulatory practices were also abundant in the Illinois River before 

that limit inputs of sediments and effl uent with the 1950s (Mills et al. 1966), but densities have high organic loads should increase water and been relatively low since then. sediment quality and help provide environmental The LTRMP data showed large differences conditions that will support healthy populations in fi ngernail clam abundances within study of mayfl ies. areas. Fingernail clams were most prevalent 

Authors in the upper three pools (Pools 4, 8, and 13; 

Jennifer Sauer, Therese Dukerschein, and Figure 2.17) with lower numbers in downstream 

Sandra Brewer. areas, especially Pool 26 and the Open River 

Reach. The only signifi cant trend observed 

2.7.2 Fingernail Clams was a marginally signifi cant positive trend 

in Pool 8 where fi ngernail clam density was 

Assessment consistently low (mean 13 m-2) from 1993 to 

Status: Mixed. The greatest number of 1998 but increased to a mean of 347 m-2 during 

fi ngernail clams were observed in the Upper 1999–2004, a 25-fold increase. Gray et al. (2005) 

Impounded Reach and numbers are low in Pool reported mean fi ngernail clam counts were 

26, La Grange Pool, and the Open River Reach. negatively associated with inorganic suspended 

Trend: Slight improvement in Pool 8, stable solid levels in Pool 8. 

in other areas. The densities of fi ngernail clams reported 

by the LTRMP are within the ranges reported Purpose in other studies (Sauer 2004). The fl uctuations The main objective of the LTRMP indicate that fi ngernail clams are able to rebound macroinvertebrate component is to provide a if conditions are right even when population better understanding of the conditions needed levels are low, such as in the southern reaches. to support viable populations of benthic 

invertebrates that are important foods for native Future Pressures

fi shes and migrating waterfowl. There is no current management objective for 

As with mayfl ies, a number of studies have fi ngernail clam abundance in the UMRS. Various 

shown that fi ngernail clams are ecologically factors may have negative effects on fi ngernail 

important as food for fi sh and waterfowl (Jude clam populations including high inorganic 

60
Figure 2.17. Estimated density of fi ngernail clams (Musculium transversum; no/m2

 ±1 standard error) weighted by area of strata within 

each Long Term Resource Monitoring Program study area from 1993 to 2004. The black lines in the graph for Pool 8 indicate a signifi cant 

increasing trend with 90% confi dence intervals. In Pools 4 and 26 and La Grange Pool, density of fi ngernail clams was not estimated in 

2003. 

61
suspended solids, high un-ionized ammonia and fi ngernail clams, projects that affect any of these 

metal concentrations, and low dissolved oxygen factors may help increase abundances.

(Sandusky and Sparks 1979; Sparks 1980; Gray Authors et al. 2005). Although habitat rehabilitation Jennifer Sauer, Therese Dukerschein, and projects are generally not aimed specifi cally at Sandra Brewer.

62
2.8 Fish Indicators 2.8.1 Bluegill

Fishes are among the most importan t Assessment 

river biota from a recreational and economic Status: Mixed. Bluegills were most standpoint. Their distribution and abundance abundant in the Upper Impounded Reach and are affected by a wide array of factors that La Grange Pool where backwater habitats are infl uence their life cycles. A diverse and healthy most abundant. Abundance is much lower in Pool fi sh community generally indicates a diversity 26 and the Open River Reach. of habitats and important river functions. Work Trend: Mixed. Most areas were stable, but by LTRMP researchers has shown that in the increasing trends were observed in Pools 4 and 8. UMRS, river reaches with the greatest variety of 

habitats, including main channel, side channels, Purpose

and backwaters, have the greatest variety of fi sh Bluegills are a major component of the 

species (Koel 2004). Changes in abundance of recreational fi shery within the UMRS and are a 

an individual species may be important for sport characteristic species of backwater environments 

anglers, but from a community perspective, when because all major life cycles typically occur 

one species is reduced, other similar species can within these habitats. Correspondingly, the public 

often increase to maintain the important functions perceives the ecological health of the UMRS, 

within communities. Long term changes or in part, by the abundance of bluegill. Tracking 

consistent differences among fi sh populations bluegill catch-per-unit-effort (CPUE) provides 

and communities may indicate differences in direct information on this resource and may 

fundamental drivers or processes. provide insight into habitat quality. The indicator 

The fi sh indicators in this report represent is the pool-wide CPUE (number/15 minutes) 

groups of fi shes with different characteristics of adult bluegills >150 mm (the minimum size 

and roles within the river ecosystem. Bluegills, generally acceptable to anglers) captured by day 

channel catfi sh (Ictalurus punctatus), and electrofi shing. 

sauger (Sander canadense) are important sport State of the Ecosystem fi shes. Sauger and catfi sh represent fi shes found 

mainly in channels, whereas bluegills represent Bluegills are perennially present in all six 

backwater fi shes. Channel catfi sh are also LTRMP study areas and are not geographically 

caught commercially as are smallmouth buffalo constrained within the UMRS (Ickes et al. 2005). 

(Ictiobus bubalus), which are fi sh characteristic However, the average abundance of bluegill 

of large rivers and are found in both channel and varies notably among the six LTRMP study areas 

off channel areas. The indicator for recreationally (Figure 2.18). Spatial differences in bluegill 

and commercially harvested fi shes includes all abundance refl ect, in part, differences in the 

native species caught for sport or for sale. The amount and quality of backwater environments 

forage fi sh index consists of the fi sh that are most in the UMRS. The 12-year mean CPUE of adult 

often food for other fi shes. Nonnative fi shes (>150 mm) bluegill is highest and most similar 

are species from other waters that have found in Pools 8 and 13, marginally lower in Pool 4 

their way into the UMRS and established new and La Grange Pool, and notably low in Pool 26 

populations. Species richness is the number of and the Open River Reach. Thus, bluegills 

species collected in each study area as an achieve their highest abundance in reaches 

indicator of the diversity of the fi sh community. where backwaters are most prominent (Pools 

When compared to historical records, LTRMP 4, 8, and 13 and La Grange Pool). Differences 

data indicate that almost all fi sh species known in bluegill abundance among these four study 

from the UMRS over the past 100 years still areas generally corresponds with the presence 

occur in the river today, although 39 species and abundance of aquatic vegetation (highest 

collected by the LTRMP were considered rare, in Pools 8 and 13, somewhat lower in Pool 4, 

endangered, or threatened by Federal or state and rare in La Grange Pool; see section 2.6.1). 

agencies. Low abundance of bluegills in Pool 26 and the 

63
Figure 2.18. Catch-per-unit-effort (CPUE, mean number caught per 15 minutes ± 1 standard error) of bluegill >150-mm total length from 

1993 to 2004 in six trend areas monitored by the Long Term Resource Monitoring Program using day electrofi shing. Black lines indicate 

statistically signifi cant trends with 90% confi dence limits.

64
Open River Reach can be attributed to a lack of 2.8.2 Channel Catfi sh

connected backwaters. The only observed trends 

in bluegill abundance were increases in Pools Assessment

4 and 8. The CPUE of adult bluegill has nearly Status: Good.

tripled over the period of observation in Pool 8 Trend: Improving in Pool 4 and La Grange 

and may be a response to habitat rehabilitation Pool, stable elsewhere.

efforts in this reach. Purpose

Future Pressures Channel catfi sh is a signifi cant component 

Habitat loss appears to be the major threat of the commercial and recreational fi sheries in 

to bluegill populations in the UMRS, although the UMRS. It is a characteristic species of river 

exploitation and forage limitations may be channels so tracking CPUE of channel catfi sh 

important locally. Loss of habitat quality due to may provide insight into habitat quality of 

sedimentation in backwaters is a signifi cant threat channel environments. This indicator is the poolas are levees that eliminate access to backwaters. wide CPUE of adult (>280 mm) channel catfi sh 

In the north, sedimentation effects may be most collected in large hoop nets. Adults were selected 

acute during winter as shallower backwaters because they are the size harvested commercially 

result in cooler water temperatures, greater and recreationally.

biological oxygen demands, and greater fl ow State of the Ecosystem rates that can lead to high fi sh mortality. Suitable 

winter habitat is uncommon in some UMRS Channel catfi sh are perennially present 

navigation pools (see section 2.3.5), however, in all six LTRMP study areas and are not 

the extent to which this limits bluegill abundance geographically constrained within the UMRS 

remains uncertain. In southern portions of the (Ickes et al. 2005). While perennially present in 

system, backwaters continue to fi ll with sediment all study areas, the average abundance of channel 

at high rates and aquatic vegetation, which is catfi sh varies among the six LTRMP study areas 

important for foraging and cover structure, (Figure 2.19). Long-term catch rates range from 

has been almost entirely lost (see section 0.2 to 1.6 fi sh per unit of effort. The mean CPUE 

2.6.1). Many factors may account for changes of adult (>280 mm) channel catfi sh was highest 

in bluegill abundance, including habitat loss, in Pool 8, marginally lower in Pool 4, La Grange 

forage limitations, exploitation, and predator- Pool, and the Open River Reach, and notably 

prey dynamics (Ickes 2005). Several studies are lower in Pools 13 and 26. In Pool 4 and La 

planned or underway to better determine bluegill Grange Pool, CPUE has increased slightly, but 

population dynamics in the UMRS. These studies has remained steady elsewhere. It is unknown 

will focus on the effects of habitat rehabilitation whether these catch rates are lower than 

efforts on bluegill populations, and will historical rates because no similar data sources 

determine whether harvest, for which few data are available from earlier periods. 

are presently available, represents a signifi cant Future Pressures

constraint on bluegill populations. Finally, Channel environments have been 

in the southern reaches little improvement in signifi cantly altered to accommodate commercial bluegill populations is expected unless backwater navigation in the UMRS (Dettmers et al. 2001; areas and aquatic plant communities can be Gutreuter et al. 2003; Pinter and Thomas 2003; rehabilitated. Pinter et al. 2006). It is uncertain whether catch 

Author rates of channel catfi sh throughout the system 

Brian Ickes. refl ect these alterations. Additional pressures 

on channel catfi sh include commercial and 

recreational harvest, disturbance, or mortality 

from deep draft tow boats (Gutreuter et al. 2003), 

65
66

Figure 2.19. Catch-per-unit-effort (CPUE, mean number caught per net day ± 1 standard error) of channel catfish >280 mm total length 

from 1993 to 2004 in six trend areas monitored by the Long Term Resource Monitoring Program using large hoop nets. Black lines indicate 

potential trends with 90% confidence limits. In Pools 4, 8, and 13, sampling with large hoop nets was not conducted in 2003. Channel catfish > 280mm - Mean CPUE
altered hydrologic regimes, and barriers to Author

longitudinal migration (Wilcox et al. 2004). Brian Ickes.

Author 2.8.4 Smallmouth Buffalo

Brian Ickes.

Assessment: 2.8.3 Sauger Status: Good. Pool 26, La Grange Pool, and 

Assessment the Open River Reach exhibit marginally higher 

catch rates than the Upper Impounded Reach. Status: Good.

Trend: Mixed. Improving in Pool 4, Pool Trend: Stable in all reaches. 

26, the Open River Reach, and La Grange Pool; 

Purpose stable elsewhere.

Sauger is a characteristic species of river Purpose channels and is recreationally exploited Smallmouth buffalo is a characteristic large throughout the UMRS. Tracking CPUE of sauger river species and is commercially exploited provides direct information on the state of this throughout the UMRS. Tracking CPUE of resource and may provide insight into habitat smallmouth buffalo provides direct information quality of channel environments. This indicator is on the state of this resource and may provide the pool-wide CPUE of adult (>200 mm) sauger, insight into habitat quality of large river which is the size available for exploitation. environments. This indicator is the pool-wide 

State of the Ecosystem CPUE of adult (>280 mm) smallmouth buffalo, 

Sauger are perennially present in all six which is the size available for commercial 

LTRMP study areas and are not geographically harvest.

constrained within the UMRS (Ickes et al. 2005). State of the Ecosystem Long-term catch rates are relatively similar Smallmouth buffalo are perennially present and range between 0.2 and 0.5 fi sh per unit of in all six LTRMP study areas and are not effort among LTRMP study areas (Figure 2.20). geographically constrained within the UMRS It is unknown whether these catch rates are 

(Ickes et al. 2005). Long-term catch rates are lower than historical rates because no similar 

similar, ranging between 0.5 and 1.2 fi sh per unit data sources are available from earlier periods. 

Whereas CPUE has of effort among LTRMP study areas. Southern fl uctuated over time, no study areas exhibit marginally higher catch long-term trends in catch rates were observed. rates than northern areas (Figure 2.21). From 

Future Pressures 1993 to 2004, CPUE has increased in four of 

Channel environments have been the six study reaches (Pool 4, Pool 26, Open 

signifi cantly altered to accommodate commercial River Reach, and La Grange Pool) for unknown 

navigation in the UMRS (Dettmers et al. 2001; reasons.

Gutreuter et al. 2003; Pinter and Thomas 2003; Future Pressures Pinter et al. 2006). It is uncertain whether Smallmouth buffalo were historically relatively low catch rates of exploitable-sized much more abundant (Coker 1929), but their sauger throughout the system refl ect, in part, populations were reduced by commercial fi shing these alterations. Additional pressures on and the establishment of common carp (Fremling sauger include recreational harvest, disturbance et al. 1989). Competition with new exotic species or mortality from deep draft tow operations (e.g., silver [Hypophthalmichthys molitrix] (Gutreuter et al. 2003), altered hydrologic and bighead carp [H. nobilis]) may further regimes, and barriers to longitudinal migration marginalize this important native species (Chick (Wilcox et al. 2004). and Pegg 2001). Additional future pressures on 

smallmouth buffalo may include commercial 

67
Figure 2.20. Catch-per-unit-effort (CPUE, mean number caught per 15 minutes ± 1 standard error) of sauger >200 mm total length from 

1993 to 2004 in six trend areas monitored by the Long Term Resource Monitoring Program using day electrofi shing. 

68
Figure 2.21. Catch-per-unit-effort (CPUE, mean number caught per net day ± 1 standard error) of smallmouth buffalo >280-mm total 

length from 1993 to 2004 in six trend areas monitored by the Long Term Resource Monitoring Program using large hoop nets. Black lines 

indicate potential trends with 90% confi dence limits. For Pools 4, 8, and 13, sampling with large hoop nets was not conducted in 2003.

69
harvest, disturbance or mortality from deep draft loads and uptake rates, water residence times) 

tow operations (Dettmers et al. 2001; Gutreuter and may represent profound changes in energy 

et al. 2003), altered hydrologic regimes, and pathways and availability. Alternatively, exotic 

barriers to longitudinal migration (Wilcox et al. species may also affect forage fi shes in the future 

2004). by competing directly with them for food. Filter 

feeders, such as Asian carp, represent the greatest Author potential future threat among exotic species. Brian Ickes.

Author

2.8.5 Forage Fish Index Brian Ickes.

Assessment: 2.8.6 Species Richness 

Status: Unknown.

Trend: Stable in all reaches. Assessment: 

Status: Good. Purpose Trend: Stable in all reaches. 

The abundance of forage fi shes represents 

production at lower trophic levels, which Purpose

provides food for large predatory fi sh that The UMRS represents the center of 

are important to anglers. Major changes in freshwater fi sh diversity in North America. 

forage resources could indicate major shifts in Collectively, UMRS fi sh community contains 

ecosystem health and function. This indicator is representative species of socioeconomic value, 

the pool-wide CPUE of emerald shiner (Notropis exotic origins, and special conservation status. 

atherinoides) and gizzard shad (Dorosoma Thus, the public perceives the ecological health 

cepedianum) combined, the two most prominent of the UMRS, in part, by the diversity of fi shes 

forage fi shes in the UMRS. present. This indicator is the number of fi sh 

species observed annually in LTRMP collections. State of the Ecosystem

The forage index is highest in La Grange State of the Ecosystem

Pool, suggesting that the Illinois River exhibits Species richness is high and stable in 

greater secondary productivity than the UMR all six LTRMP study reaches, ranging from 

(Figure 2.22). All UMR study reaches had a approximately 55 to 75 species annually per 

similar mean forage index during 1993–2004. study area (Figure 2.23) with means over the 

The forage index has remained stable in all six period ranging from about 60 to 70. Annual 

LTRMP study reaches. The status of forage fi sh fl uctuations are attributed to random variation, 

is considered unknown because the adequacy unpredictable rare species occurrences, and 

of forage fi sh production to support predatory variation in sampling effort. The large reduction 

fi shes has not been determined. Thus, it is not in species richness seen in Pools 4, 8, and 13 

known whether the abundance of forage fi sh in 2003 was due to a substantial reduction in 

represents a surplus of food for predatory fi shes sampling effort in those pools due to budget cuts. 

or an inadequate level of food that may limit the The highest number of species occurred in Pool 8 

production of predatory fi sh. More work on food and the lowest in the Open River Reach. 

web interactions and fi sh growth and abundance The species present in each LTRMP study 

is needed to answer that question. area are similar to the species present 100 years 

ago. Almost all native species are still present, Future Pressures but their abundances may have been changed Major shifts in forage abundance are only from historical conditions due to habitat changes, likely to occur if major trophic pathways are competition with other species, or changes altered. Such changes would most likely occur at in river functions. One example is the highly the base of the food web due to factors affecting migratory skipjack herring (Alosa chrysochloris), primary production (e.g., sedimentation, nutrient 

70
Figure 2.22. Catch-per-unit-effort (CPUE, mean number caught per 15 minutes ± 1 standard error) of the forage index (combined CPUE 

of emerald shiner (Notropis atherinoides) and gizzard shad (Dorosoma cepedianum)) from 1993 to 2004 in six trend areas monitored by the 

Long Term Resource Monitoring Program using day electrofi shing.

71
Figure 2.23. Species richness (number of species collected annually in all sampling gears) from 1993 to 2004 in six trend areas 

monitored by the Long Term Resource Monitoring Program. The horizontal line indicates the highest mean index among all areas 

(observed in Pool 8) and is provided for reference. Stars indicate signifi cant reductions in sampling due to budget cuts.

72
which is now rare above Lock and Dam 19 Purpose

because that dam is an effective barrier to Nonnative fi shes (species originating from 

migration except in years of extreme fl ooding. outside the basin) occur in all monitored study 

Of the native fi shes observed by the LTRMP, reaches. The fraction of nonnative biomass to 

39 species have been reduced to the point that total fi sh biomass is frequently regarded as an 

they have conservation status nationally or in one indicator of ecological impairment. Nonnative 

or more UMRS states. species can compete with more desirable 

Several nonnative species have been native species, thereby reducing abundance 

added to the original UMRS community (see and distribution of natives. Tracking nonnative 

section 2.8.7). Of the 139 fi sh species collected fi sh biomass provides direct information on 

by LTRMP, 12 (9%) are nonnatives or their the prominence of nonnative species and may 

hybrids. The exotic common carp (Cyprinus indicate stresses on native fi sh assemblages. 

carpio) is now abundant throughout the system. This indicator is the proportion of total fi sh 

Moreover, exotic species introductions continue biomass composed of seven nonnative species: 

primarily from the southern reaches and from goldfi sh (Carassius auratus), grass carp 

the connection of the Illinois River with Lake (Ctenopharyngodon idella), common carp, 

Michigan through the Chicago Sanitary and silver carp, bighead carp, white perch (Morone 

Ship Canal. Presently, exotic species account for americana), and striped bass (Morone saxatilis). roughly 10% of the species richness in La Grange State of the Ecosystem Pool. 

The annual proportion of nonnative biomass Future Pressures to total fi sh biomass is sizeable, ranging from 23 

Habitat losses, impairments to long-ranging to 68%, and rivaling other systems considered 

migrations, and exotic species represent the highly impaired by nonnative species (e.g., 

most signifi cant future threats to UMRS fi sh Great Lakes). The majority of nonnative biomass 

species richness. Loss of habitat diversity, is from common carp (range 72–98% among 

fl oodplain isolation, and altered hydrology are locations). While the proportion of nonnative 

regionally and systemically important habitat biomass is high in the UMRS, this indicator is 

issues. Navigation dams are believed to restrict holding relatively steady in the lower reaches 

movements of many migratory species within and improving slightly in the upper reaches 

the UMRS. Data suggest that species are likely (Figure 2.24). Notably, Pool 8 generally has a 

to persist, but may be reduced in abundance lower proportion of nonnative biomass compared 

as a consequence of impoundment. Nonnative to other reaches and demonstrated a signifi cant 

and exotic species, such as several recently decline over 1993–2002. Weaker, yet statistically 

introduced species of Asian carp, may compete signifi cant declines occurred in Pools 4 and 13. 

with or regionally displace some native species. Reasons for these declines are unknown, but may 

Author be a function of habitat rehabilitation, predatory 

pressures on nonnative species, parasitism, Brian Ickes.

disease, or some combination of these. Research 

2.8.7 Nonnative Fishes on why the percentage nonnative biomass is 

lower and declining in upper pools, especially 

Assessment: Pool 8, may yield lessons applicable to other 

Status: Poor. Nonnative fi shes account for a river reaches.

substantial portion of total biomass in all reaches. Asian carps (bighead and silver carp) are 

Trend: Mixed. Improving in Upper recent invaders to the southern UMRS coming 

Impounded Reach, stable in Pool 26, the Open up from the lower Mississippi River. Asian carp 

River Reach, and La Grange Pool. were fi rst collected by the LTRMP in Pool 26 in 

1993. As of 2004, they have not been collected 

by LTRMP above Pool 26, but a few individuals 

73
Figure 2.24. Percentage of total fi sh biomass accounted for by nonnative species from 1993 to 2002 in six trend areas monitored by the 

Long Term Resource Monitoring Program. Red lines indicate possible trends. The horizontal line indicates the highest mean index among 

all areas (observed in Pool 26), and is provided for reference. 

74
have been collected by other means as far 

north as Pool 4. Their dispersal into the Upper 

Impounded Reach may be slowed at Lock and 

Dam 19. This dam has the highest head (36 feet) 

among dams in the mid-portion of the system 

(higher dams exist at the extreme upper end of 

the navigation system) and is a more substantial 

barrier to fi sh migration than other dams (Wilcox 

et al. 2004). Asian carps have achieved notable 

abundance in the lower reaches of the UMRS, 

which has been widely reported in the media, 

and are now commercially harvested in those 

areas. However, LTRMP sampling methods are 

relatively ineffective at collecting these species, 

so our estimates of their proportion in the total 

catch are probably low. Thus, although no trends 

were apparent in our data from the southern 

reaches, our estimates of Asian carp biomass may 

be low and the percentage of nonnative biomass 

may actually be increasing in these reaches. The 

LTRMP sampling will continue to provide an 

index of nonnative biomass useful for comparing 

among study areas, but questions specifi c to the 

abundance of Asian carps may require sampling 

by other methods.

Future Pressures

Nonnative fi shes compose a sizeable 

fraction of the total fi sh biomass in the UMRS 

and new introductions have occurred recently. 

Once established, nonnative species are nearly 

impossible to control, and then only at great 

expense. The Mississippi River and its principal 

tributaries provide a highway for nonnative 

species to travel from areas as geographically 

disparate as the Atlantic Gulf Coast and the 

Laurentian Great Lakes to the interior of the 

North American continent. Recently established 

populations of silver and bighead carp in the 

southern portions of the UMRS are expected 

to increase in abundance (as evidenced by 

more recent data from the lower reaches) and 

expand their distribution within the UMRS. 

Additional species including round goby 

(Neogobius melanostomus) and black carp 

(Mylopharyngodon piceusare) are poised to 

invade the UMRS from Great Lakes and down 

river sources, respectively. Because of the ability 

of many nonnative fi sh species to compete 

with and displace native species, nonnative 

species will remain a principal threat to native 

biodiversity in the foreseeable future in the 

Mississippi River drainage, home to nearly onethird of the entire North American freshwater fi sh 

fauna.

Author

Brian Ickes.

2.8.8 Recreationally Harvested Native Fishes

Assessment

Status: Fair for all reaches. All reaches 

support recreationally harvested fi shes and 

recreational fi sheries. 

Trend: Mixed. Stable or increasing in the 

three upper pools; stable or declining in the lower 

reaches.

Purpose

The production of recreationally harvestable 

fi shes is one of the important services that the 

UMRS ecosystem provides to humans. Tracking 

CPUE of recreationally harvested fi shes provides 

direct information on this resource and may 

provide insight into habitat quality. This indicator 

is the combined CPUE from 19 native fi sh 

species (Table 2.3) and includes fi shes common 

in backwaters and channel habitats. 

Table 2.3. Common and scientifi c names of the 19 species that 

were combined to create an index for recreationally harvested 

fi shes. 

Common name Scientifi c name

Northern pike Esox lucius

Channel catfi sh Ictalurus punctatus

Blue catfi sh Ictalurus furcatus

Flathead catfi sh Pylodictis olivaris

Freshwater drum Aplodinotus grunniens

White bass Morone chrysops

Yellow bass Morone mississippiensis

Smallmouth bass Micropterus dolomieu

Largemouth bass Micropterus salmoides

Rock bass Ambloplites rupestris

White crappie Pomoxis annularis

Black crappie Pomoxis nigromaculatus

Green sunfi sh Lepomis cyanellus

Bluegill Lepomis macrochirus

Redear sunfi sh Lepomis microlophus

Pumpkinseed Lepomis gibbosus

Yellow perch Perca fl avescens

Sauger Sander canadense

Walleye Sander vitreus

75
State of the Ecosystem

La Grange Pool of the Illinois River had the 

greatest average CPUE of recreational fi shes 

(Figure 2.25). Environmental conditions and 

the overall health of the fi sh community in the 

Illinois River have increased since the early 

and mid-1900s, but are still not comparable 

to the excellent fi shery that occurred in the 

late 1800s (Pegg and McClelland 2004). 

Whether populations can be returned to those 

levels is unknown. The Open River Reach had 

the lowest abundance of recreational fi shes, 

which would be expected because the lack of 

backwater habitats in that reach means that the 

recreational fi shes associated with those habitats 

are virtually nonexistent. Therefore, different 

levels of this indicator would be expected among 

study reaches, but all reaches were considered 

fair because there appears to be potential for 

improvement in each reach. 

Trends for recreationally harvested fi shes 

varied longitudinally. In the three northern 

LTRMP study reaches (Pools 4, 8, and 13), 

CPUE levels for recreationally harvested fi shes 

were increasing or holding steady (Figure 2.25). 

For the three southern LTRMP study reaches 

(Pool 26, La Grange Pool, and the Open River 

Reach), CPUE of recreationally harvested fi shes 

is declining or holding steady. 

 Future Pressures

Habitat degradation and invasive species 

appear to be the largest threats to recreationally 

harvested fi shes. Backwaters continue to fi ll with 

sediment and, in southern portions of the system, 

aquatic vegetation has been almost completely 

lost. A variety of habitat rehabilitation projects 

have been constructed in the UMRS aimed at 

increasing abundance of recreational fi shes. 

Some of these projects have been successful 

at increasing fi sh abundance locally, but their 

effects at the reach scale or larger are not yet 

evident. The LTRMP will be able to detect these 

effects when suffi cient numbers of projects have 

been constructed to elicit reach-wide effects 

in the LTRMP study areas. Among LTRMP 

locations, Pools 8 and 13 and La Grange Pool 

have been the sites of the greatest number of 

habitat rehabilitation projects and are the most 

likely candidates for initially detecting a poolwide effect. 

Author

John Chick.

2.8.9 Commercially Harvested Native Fishes

Assessment 

Status: Fair for all reaches. All reaches 

support commercially harvested fi shes and 

commercial fi sheries. 

Trend: Mixed. Catches have declined in 

Pool 8, but are stable in all other reaches. 

Purpose

Commercial fi sheries exist throughout the 

UMRS, and the production of commercially 

harvestable fi shes is one of the important services 

provided by this ecosystem. Tracking CPUE 

of commercially harvested fi shes provides 

direct information on this resource, and may 

provide insight into habitat quality and the 

likelihood of overharvest. This indicator is the 

combined CPUE from seven native fi sh species 

(Table 2.4). Common carp and Asian carps are 

also commercially harvested, but are nonnative 

species and are not included in this indicator.

Table 2.4. Common and scientifi c names of the seven native 

species that were combined to create an index for commercially 

harvested fi shes. Note that some commercially harvested species 

are also harvested by recreational fi shers and are included in the 

recreationally harvested fi shes indicator.

Common name Scientifi c name

Bigmouth buffalo Ictiobus cyprinellus

Smallmouth buffalo Ictiobus bubalus

Black buffalo Ictiobus niger

Channel catfi sh Ictalurus punctatus

Blue catfi sh Ictalurus furcatus

Flathead catfi sh Pylodictis olivaris

Freshwater drum Aplodinotus grunniens

State of the Ecosystem

The highest CPUE of commercially 

harvested fi shes occurred in La Grange Pool 

in the Illinois River (Figure 2.26). Historical 

commercial fi sheries data indicate that the 

overall productivity of the Illinois River was 

76
77

Figure 2.25. Catch-per-unit-effort (CPUE, number/15 min +/- 1 standard error) of recreationally harvested fi shes caught with day 

electrofi shing from 1994 to 2004 by the Long Term Resource Monitoring Program. Red lines indicate signifi cant trends. Horizontal lines 

indicate the overall mean CPUE from La Grange Pool (the highest mean), and are provided for reference.
substantially greater in the late 1800s, with Future Pressures

commercial harvest at least 10 times greater The overall effort and infrastructure 

than recent catches (Sparks 1992; Pegg and associated with commercial fi sheries in the 

McClelland 2004). Although environmental UMRS are at relatively low levels and are 

conditions and the overall health of the fi sh unlikely to expand greatly in the foreseeable 

community in the Illinois River have improved future. For the seven species composing this 

since the establishment of the Clean Water Act indicator (Table 2.4), habitat degradation and 

(Pegg and McClelland 2004), productivity has invasive species appear to be the most important 

not returned to historical levels. The maximum future threats. Most of the rehabilitation projects 

production for commercial fi shes in different designed to improve fi sh habitat in the UMRS 

reaches of the UMRS is unknown. However, have been planned for recreational species. It 

based on the history of the Illinois River, there is unknown whether managing primarily for 

appears to be potential for greater production. recreational species might increase production 

Therefore, the status of commercially harvested of all fi shes, or might transfer production 

species was designated fair for all reaches. from commercial to recreational fi shes. If the 

In fi ve of the LTRMP study reaches, CPUE abundance of commercially harvested species 

levels for commercially harvested fi shes were declines in the future as a result of habitat loss, 

stable (Figure 2.26). Therefore, we have little managers may need to develop new types of 

evidence of habitat problems or overharvest for habitat projects focused on commercial fi shes.

these reaches. A negative trend was observed Author in Pool 8 and may be a cause for local concern. 

Managers may want to assess whether there are John Chick.

habitat issues specifi c to commercially harvested 

fi shes that need to be addressed in Pool 8. 

78
Figure 2.26. Catch-per-unit-effort (CPUE, number/15 min +/- 1 standard error) of commercially harvested fi shes caught with day 

electrofi shing from 1994 to 2004 by the Long Term Resource Monitoring Program. Red lines indicate signifi cant trends. Horizontal lines 

indicate the overall mean CPUE from La Grange Pool (the highest mean) and are provided for reference. 

79

Chapter 3. Discussion, Conclusions, and Recommendations

The Ecological Status and Trends of the EMP through, for example, changes in dam 

Upper Mississippi River 1998 (USGS 1999) operations, modifi cations to channel structures, 

provided a broad-based assessment of ecosystem restoring fl oodplain connectivity, or changing 

health of the four river reaches within the UMRS. fl ow distribution. The LTRMP can assess how 

The fi rst report used six criteria for ecosystem successful those techniques are at enhancing 

health to assess the condition of each reach and ecosystem health and sustainability in the long 

to forecast future conditions. The current report term. 

builds upon that synthesis by using a 10+year 3.1.2 Comparison of Status and Trends among record of data collected by the LTRMP. The Regions and Indicators report presents measurements of river health 

through the use of indicators and conveys this When the indicators used in this report are 

information with scientifi c interpretations that viewed together, they reveal a system with both 

refl ect declining, stable, or improving conditions. good and poor characteristics (Figure 3.1). The 

The fi ndings of this report are being used to indicators for sedimentation, major nutrients, and 

track progress toward reaching system goals and fl oodplain forests are poor to mixed throughout 

objectives, and refi ning indicators, as needed. the system and in most locations these indicators 

show a decline in condition. Indicators for 3.1 Integrity and Sustainability of the Upper dissolved oxygen levels, species richness of Mississippi River System fi shes, and population of some fi sh species 

are good to mixed throughout the system with 3.1.1 Implications for Ecosystem Integrity and some increasing trends. All other indicators are Sustainability fair to mixed, with some indicators showing 

The LTRMP data indicate a gradient of both positive and negative trends. The spatial 

river health within the UMRS ranging from a differences seen within and among indicators 

relatively healthy system in the northern reaches, reveal patterns related to the health of specifi c 

to a system that is much less healthy in the reaches as detailed below. 

south. This diversity of conditions makes the Previous analyses of LTRMP data have 

UMRS a mirror for many other rivers throughout shown that different reaches of the UMRS can 

the world and an excellent laboratory for be identifi ed based on geomorphic features 

development of effective restoration strategies. (Knox 2000), habitats (Koel 2001), and fi sh 

The good news is that, compared to many of species (Koel 2004; Chick et al. 2006). The 

the world’s temperate-zone rivers, many parts data presented in this report support this reachof the UMRS still retain the basic features based approach to understanding and managing 

that defi ne river ecosystem integrity, such as a the system, but also show that some indicators 

fairly natural discharge regime, ability to move are fairly consistent throughout the system. 

sediments through most dams, a nearly complete Overall, results demonstrate that environmental 

species complex, and a natural range of water conditions are best in the Upper Impounded 

temperatures. However, the system has some Reach, where habitat diversity is greatest and 

problems that need to be addressed to improve the river maintains more of its connection to 

ecosystem health. the fl oodplain. Conditions gradually decline 

Reducing stressors on the river ecosystem downstream as habitat diversity is lost, the river 

will require a cooperative effort among many becomes more isolated from its fl oodplain, and 

agencies, especially for stressors that operate public land is rare.

mainly in the uplands and tributaries. However, Hydrologic data show that, compared to 

many stressors that operate within the channel pre-dam conditions, the impounded reaches 

or fl oodplain can be addressed directly by the had higher average water elevations, especially 

81
82

he Long Term Resource Monitoring Program (LTRMP) on the 

nd of a bar indicates a trend in that direction for that sampling area 

he text for details on the locations of the study areas (Chapter 1) and 

Comparison of ratings of the status and trends for resource indicators derived from data collected at the six study areas of t Figure 3.1.

Upper Mississippi River System. The black bars indicate the range of status within that LTRMP sampling areas. An arrow at the e(or at least one sampling areas in the left panel). A question mark means that rating of that indicator was not possible. See t

 c ratings (Chapter 2). reasons for specifi

Pools 4, 8, and 13 

(Upper impounded) 

 Pool 26 

(Lower impounded) 

 Open River Reach 

(Unimpounded) 

 La Grange Pool 

(Illinois River) 

Indicator group

Poor 

Mixedpoor Fair Mixed- good Good Poor Mixed- poor Fair Mixed- good Good Poor Mixed- poor Fair Mixed- good Good Poor Mixed- poor Fair Mixed- good Good 

Hydrology Indicators Annual discharge  Seasonal water elevation Water Quality Indicators  Nitrogen  Phosphorus  Chlorophyll a Total suspended solids 

 Dissolved oxygen 

 Suitable winter habitat Sedimentation Indicators  Depth diversity - impounded areas  Sedimentation in backwaters Land Cover/Land Use Indicators  Floodplain forest  Emergent vegetation  Area behind levees Aquatic Vegetation Indicator  Submersed aquatic vegetation Macroinvertebrate Indicators  Burrowing mayflies  Fingernail clams Fish Indicators  Bluegill  Channel catfish  Sauger  Smallmouth buffalo  Forage fish index ? ? ? ? Species richness  Nonnative fishes  Recreationally harvested fishes  Commercially harvested fishes 
during low fl ow periods (Figure 2.2). In the impounded areas. Studies by the LTRMP indicate 

Unimpounded Reach, the annual cycle of water that sedimentation rates are highly variable 

elevations was similar between pre- and post- (Figure 2.11) but the net effect over 50 years 

dam periods (Figure 2.2), but channel shape was a substantial loss of habitat diversity 

and hydraulics have been substantially altered (Figure 2.10). For highly variable processes, such 

from historical conditions. All reaches have as sedimentation, the time span of the LTRMP 

experienced increased short-term variation in data is not long enough to make defi nitive 

water levels. Factors contributing to increased statements about present trends. We expect 

variation include increased runoff from uplands sedimentation to continue, but at a slower rate 

and urban areas, dam operations, and channel because as sedimentation continually reduces 

narrowing. These factors represent hydrologic the volume of pools, trapping effi ciency for 

stressors to the river, but they can be managed additional sediment is also reduced. Some of 

to some degree in the impounded reaches by this lost habitat diversity can be restored through 

changes in dam operations to dampen water level management techniques, such as constructing 

fl uctuations (Landwehr et al. 2005). islands, dredging backwaters, and restoring 

When the navigation dams were fi rst built fl oodplain connections. In some instances, 

on the UMRS, there was an increase in habitat changes in habitat diversity may be substantial 

diversity due to initial fl ooding of terrestrial and quick, such as removing a levee to reclaim 

areas. However, since that initial increase, habitat a levee district, which can affect a large area 

diversity has been lost throughout the UMRS. with a single action. However, for smaller-scale 

This is a serious management concern because projects (e.g., island building), it will likely 

previous analyses have shown that fi sh species require multiple projects constructed over many 

diversity is directly related to habitat diversity years to produce a signifi cant change in habitat 

(Koel 2004). In the impounded reaches, the diversity. Both types of change can be identifi ed 

dams themselves caused changes in various within LTRMP focal pools as longer data sets are 

processes (e.g., sediment dynamics, water levels, developed. 

wind fetch) that act over the long term to reduce The LTRMP data show that water quality 

habitat diversity. Obviously, the Unimpounded among the four river reaches can be extensively 

Reach did not experience the one-time increase different for some indicators, but similar for 

in habitat diversity associated with dams, but it others. The most substantial difference is in the 

has still experienced loss of habitat diversity. concentration of total suspended solids (TSS). 

Besides dam building, there are a variety The TSS drop from upper Pool 4 to lower Pool 4 

of processes that effect habitat diversity. Most because Lake Pepin, a natural lake on the river, 

of these processes operate slowly and some serves as an effi cient trap for suspended solids. 

can exhibit high annual variation. Building The TSS then increase from about 20 mg/L in 

levees, which was more prevalent in the lower lower Pool 4 to 200 mg/L in the Open River 

reaches, eliminated connections of the river Reach and is intermediate in the Illinois River 

to its fl oodplain, thus eliminating much of the (Figure 2.6). In lower Pool 4 and Pool 8, TSS 

highly diverse, seasonally fl ooded habitat from are generally below the recommended maximum 

the ecosystem. Channelizing the river with wing concentration for plant growth of 25 mg/L 

dikes and closing structures also reduces the (summer average, UMRCC 2003). In Pools 

ability of biota to access off-channel habitats. 4 and 8, TSS exhibit a downward trend since 

This is evident in all reaches, but especially in 1994 for unknown reasons. In upper Pool 4 and 

the lower reaches where sedimentation has fi lled in Pool 13, TSS exceed the maximum during 

in the area between most wing dikes and cut off spring and summer of most years, whereas the 

access to many side channels. three lower reaches are above the maximum 

In all reaches, sedimentation has fi lled- virtually all the time. This downstream increase 

in backwaters and deep areas and erosion in TSS is a common feature of rivers but is 

has eliminated many islands, especially in likely exacerbated in the UMRS by runoff 

83
from agricultural watersheds, which are more lawns. In addition, because phosphorous is 

prevalent in the lower reaches. typically adsorbed onto sediment particles, any 

Because high TSS concentrations reduce management that helps to reduce suspended 

light penetration into the water, they are one of sediments will also tend to reduce phosphorous. 

the primary causes of differences in submersed Nitrogen can be reduced by management 

aquatic vegetation among these reaches. that moves more water through wetlands and 

Submersed vegetation is virtually absent from shallow aquatic areas (either in the watershed 

the three lower reaches (Figure 2.15) where or fl oodplain) where natural processes will 

TSS concentrations are too high to allow light convert the nitrogen to a gas, which is then lost 

to penetrate and seeds to germinate. In the to the atmosphere. Management of the UMRS 

Unimpounded Reach below the Missouri River, to divert more water from the main channel 

TSS have always been high and vegetation has into off channel areas will help reduce nitrogen. 

never been abundant. However, it is highly unlikely that working in 

Reducing the TSS load to the impounded the fl oodplain of the UMRS alone will reduce 

reaches will be diffi cult but may result from nitrogen enough to eliminate hypoxia in the Gulf 

increased use of best management practices on of Mexico (Mitsch et al. 2001; Richardson et al. 

the watershed or from restoration of tributary 2004). 

deltas in the UMRS fl oodplain to trap sediments High nutrient concentrations can cause 

on the land before they enter the river. However, excess plant growth. However, LTRMP data on 

even without reducing the overall sediment chlorophyll in the main channel (Figure 2.5) 

load, certain management techniques, such show that all reaches are typically within the 

as building islands, can create areas that are medium (mesotrophic) range designated by 

sheltered from current and wind, which allows Dodds et al. (1998). Thus, although nutrient 

suspended sediments to settle out and increase levels in the UMRS are high, algal growth is 

light penetration. These techniques have worked typically not excessive. However, algae blooms 

well in the Upper Impounded Reach and should (a locally high abundance of algae) sometimes 

be evaluated in lower reaches. occur in the UMRS and can have negative 

The nutrient phosphorous, which is effects. Blooms usually occur when fl ow is low. 

associated with sediment particles, also Low fl ows mean that water stays in one place 

increases downstream from about 0.1 mg/L in longer, which allows algae to grow quickly. 

the Upper Impounded Reach to 0.25 mg/L in Abundant algae, especially in combination with 

the Open River Reach (Figure 2.4). Nitrogen high suspended solids, reduce light penetration 

concentrations increase from about 2 mg/L in and thus, growth of rooted aquatic plants. In 

the Upper Impounded Reach to 3 mg/L in the addition, blooms are often composed of mainly 

lower reaches (Figure 2.3). The Illinois River blue-green algae, whose value as food for other 

generally has the highest concentrations of both biota is quite low. More work is needed on the 

nitrogen (4 mg/L) and phosphorous (0.4 mg/L). species composition and production of the algal 

Mean phosphorus concentrations are above community under different combinations of 

the suggested upper limit (0.08 mg/L; USEPA fl ow and nutrient loads to determine potential 

2000a; Smith et al. 2003) for nearly all reaches ecological effects. 

and years. Mean nitrogen concentrations in pools Previous modeling (Best et al. 2004a, b; 

of the Upper Impounded Reach are above the Yin and Langrehr 2005) has shown that the 

suggested upper limit (2.18 mg/L; USEPA 2000a; distribution of submersed aquatic macrophytes 

Smith et al. 2003) about 50% of the time, but in can be largely explained by transparency, 

the lower reaches, nearly all the time. water depth, and current velocity. As already 

Reducing nutrient loads to the river could discussed, some of these relations can be seen in 

be achieved by more effective waste treatment the LTRMP indicator data and in evaluations of 

for point source inputs and by reducing rehabilitation projects (Langrehr et al. 2007). But 

loss of nutrients applied to farm fi elds and in addition, variation in water levels can reduce 

84
85

abundance of both submersed and emergent LTRMP (Figures 2.16 and 2.17) but have been 

aquatic macrophytes. consistently higher in the Upper Impounded 

The LTRMP land cover data indicate that Reach where silt-clay substrates are more 

between 1989 and 2000, emergent vegetation abundant. These organisms are important foods 

decreased in most pools of the Upper Impounded for fi sh and waterfowl. For example, data from 

Reach but generally increased in all other the U.S. Fish and Wildlife Service indicate that 

reaches. Determining the cause of changes at diving ducks in Pool 8 were more abundant 

two points 10 years apart is diffi cult. However, in years when fi ngernail clams were prevalent 

as more management actions, such as summer (Figure 3.2). 

drawdowns, island building, and changes in Benthic invertebrates are one of the few 

control point are implemented, future data may biological indicators for which quantitative 

be able to correlate these actions with changes data exist before LTRMP (Sauer 2004). The 

in land cover. More rapid evaluation will be abundances seen in LTRMP data are within 

possible for actions implemented on LTRMP the ranges seen in these earlier studies. These 

sampling areas, such as island building in organisms are sensitive to shifts in environmental 

Pool 8 (Langrehr et al. 2007) and the summer quality and can rapidly disappear from areas 

drawdowns conducted on Pool 8 in 2001 where conditions become unfavorable, but they 

and 2002. The effect of these or any other also have the potential to rebound rapidly if 

management actions implemented in LTRMP conditions improve. 

sampling areas, can be addressed by looking Analyses of LTRMP data by Gray et al. 

at changes over subsequent years in various (2005) showed that abundance of fi ngernail 

indicators, the persistence of any effects through clams was negatively associated with levels 

time, and possible time lags of responses. of inorganic suspended solids (silt and 

A primary factor for distribution of benthic clay particles) in Pool 8. This suggests that 

invertebrates is substrate type. Densities of management to reduce inorganic suspended 

fi ngernail clams and burrowing mayfl ies have solids may increase fi ngernail clam densities. 

been highly variable over the span of the But, given the annual variability in abundance 

1996 1997 1998 1999 2000 2001 2002

Density per meter squared

Pool 8 closed area

0

200

400

600

800

1000

1200

1400

Fall Diving Duck Numbers

(Pool 8 closed area)

0

20000

40000

60000

80000

100000

120000

140000

160000

Mayflies

Fingernail clams

Diving Ducks

Fall 1998

Spring 1999

Figure 3.2. Data on density of fi ngernail clams (Musculium transversum) and mayfl ies (Hexagenia spp.) from the Long Term Resource 

Monitoring Program compared to total number of diving ducks such as scaup (Aythya sp.) and ring-necked ducks (Aythya collaris) observed 

(data from U.S. Fish and Wildlife Service) in the area of Pool 8 that was closed to hunting, 1996–2002. Invertebrate sampling is conducted 

in spring of each year, but indicates abundances the previous fall. Thus, diving duck numbers were correlated with densities of fi ngernail 

clams, an important food source for the ducks.
documented by the LTRMP, it would likely that they can be successful at increasing fi sh 

take many years to reliably identify any trends abundance locally. But, to determine if such 

in invertebrate abundance resulting from efforts will result in systemic rehabilitation, we 

management. need to know if these actions merely redistribute 

A variety of different analyses of the fi sh existing fi sh populations or can actually increase 

indicators have concluded that at large spatial fi sh production within an entire reach. Below, we 

scales, there is a general north-south dichotomy discuss one such possibility in Pool 8. 

in UMRS fi sh communities. A northern fi sh Among individual species of fi sh, there were 

community, dominated by fi sh associated with some signifi cant trends identifi ed, but for most 

backwater and lake-like habitats (e.g., bluegills, the cause is unknown. For example, smallmouth 

largemouth bass (Micropterus salmoides), buffalo showed signifi cant increases in catch 

various minnows and shiners) differs from the rates in all study areas except Pools 8 and 13 

southern fi sh community that is more associated (Figure 2.21) for unknown reasons. Recreational 

with main channel and side channel habitats (e.g., fi shes showed an increase in Pool 8, but 

gizzard shad, buffalo [Ictibus spp.], white bass decreases in La Grange Pool and the Open River 

[Morone chrysops]). However, species richness Reach. 

(the number of different species collected) was Determining the potential causes for 

similar and stable among study area ranging from changes in a single species or assemblage has 

about 55 to 75 per year. many potential pitfalls and is not likely to be 

There are many reasons why this north- an effective exercise unless there is reason to 

south gradient might develop, including climate, suspect specifi c factors. That may be the case for 

temperature, and habitat differences. Differences bluegills in Pool 8, which showed a signifi cant 

in winter habitat from north to south seem a increase in abundance since the late 1990s 

possible reason. However, LTRMP data show (Figure 2.18). This increase may be associated 

that pools in the Upper Impounded Reach have with HREP projects to construct islands in the 

the least amount of suitable habitat, but support pool and improve backwater habitats. More 

considerably high abundances of bluegills than specifi c analyses of Pool 8 data are required to 

Pool 26 (Figure 2.18) where winter conditions investigate this possibility. Additional island 

are more suitable. Biologists know that winter building is planned for Pool 8 in the next few 

can be a physiologically stressful time for fi shes years, which should increase the effect if it 

and that fi sh gather in dense aggregations in exists, and continued LTRMP data collection 

suitable habitat during winter. But apparently, a will increase our ability to identify that effect. 

limited area of suitable winter habitat can support However, any such analysis should attempt to 

relatively large bluegill populations. Previous account for confounding factors, such as the 

analyses of LTRMP data investigated the relation summer water drawdown conducted on Pool 

between abundance of bluegills and similar fi shes 8 in 2001–2002, and for regional effects by 

to general availability of backwaters, but not comparing results from other locations (Pool 4 

winter habitat specifi cally (Gutreuter 2004). The also exhibited a signifi cant increase in bluegill 

results indicated that lack of backwaters was a catch during the same period). The 10 years of 

limitation only when backwaters were extremely LTRMP data currently available can suggest 

scarce (less than about 3% of total fl oodplain potential trends for further investigation (as 

area). indicated by the analyses of backwater habitats 

Further insight into factors limiting sunfi sh across pools discussed above), but are not likely 

populations will probably not come from broad to provide defi nitive results.

analyses of monitoring data, but will likely The LTRMP data show that nonnative 

result from evaluations of management actions fi shes compose a high percentage of total fi sh 

within a single pool that are designed to improve biomass (Figure 2.24). A high percentage of 

backwater habitats. Evaluations of these types of nonnative fi shes in the community is generally 

management actions within the UMRS indicate considered an indicator of ecological impairment. 

86
The annual proportion of nonnative biomass in (Figure 2.25); and isolation of the fl oodplain 

LTRMP catches ranged from 23% to 68% among from the river is much more prevalent in the 

pools and averaged about 50%. Pool 8 has been lower reaches. Some of these conditions may 

consistently lower than other pools, but still be associated with natural gradients within the 

ranged from 23% to 44%. Most of the nonnative river system, but in general, the LTRMP data 

biomass is due to common carp. Although no show more impaired ecological condition in 

specifi c targets for percentage of nonnative the lower reaches relative to the upper reaches. 

fi shes have been identifi ed by managers, it is Rehabilitating the system will require effort in 

likely that 50% would be considered too high. A all reaches. However, the challenges appear to 

positive note is that the three pools in the Upper be more daunting in the lower reaches as many 

Impounded Reach (Pools 4, 8, and 13) all showed of the stressors and drivers are more highly 

signifi cant decreases in percentage of nonnative modifi ed there.

biomass over time. Further analyses of LTRMP 3.2 Use and Application of LTRMP data may reveal possible factors that correlate Component Data with nonnative biomass and suggest management 

strategies that might reduce nonnative Data collected by the LTRMP staff have been 

abundance. However, the reasons for changes in vital for a number of UMRS ecological efforts. 

fi sh communities are complex and monitoring The use of this information varies, but can be 

data alone cannot confi rm cause-and-effect categorized into three primary areas that include 

relations. Experiments using various techniques developing a better understanding of the UMRS 

to attempt to reduce nonnative biomass will be ecosystem and its condition, improved planning 

needed along with focused studies to assess the and decision making, and enhanced rehabilitation 

direct effects of each technique. The LTRMP data and management of UMRS ecological resources. 

will be needed to assess longer-term effects and 

provide the information needed to turn short- 3.2.1 Condition of the Ecosystem

term, local experiments into long-term, reach- Status and Trends Reports wide management strategies for both native and 

nonnative species. This report and the 1998 Status and Trends 

Taken together, these indicators document Report (USGS 1999) were developed to 

ecological impairments in all parts of the system, provide an assessment of the UMRS ecosystem 

but show that the health of the system’s lower condition. Data collected by the LTRMP were 

reaches is substantially worse than the Upper summarized with an emphasis on describing 

Impounded Reach. In addition, a number of the status and trends of UMRS natural 

improving trends are evident in the upper reach, resources. An effort was made to explain river 

but few in the lower reaches. Specifi cally, ecosystem disturbances when possible (i.e., 

concentrations of major nutrients (nitrogen and Why was this trend occurring?) to help river 

phosphorus) are notably higher in lower reaches stakeholders consider if and what future actions 

compared to upper reaches (Figures 2.3 and are necessary. These status and trends reports 

2.4); suspended solids are consistently high in provide information that will help refi ne future 

lower reaches but are declining in Pools 4 and 8 monitoring, research, and rehabilitation efforts. 

(Figure 2.6); aquatic vegetation is virtually absent UMRS Habitat Needs Assessment

from the lower reaches (Figure 2.15); aquatic The primary objectives of the Habitat Needs invertebrates associated with soft sediments are Assessment (HNA; Theiling et al. 2000; USACE much less abundant in lower reaches (Figures 2000) were to evaluate the existing habitat 2.16 and 2.17); the percentage biomass of conditions throughout the UMRS, forecast future nonnative fi shes is declining (i.e., improving) in habitat conditions, and quantify ecologically the upper reaches, but not in the lower reaches; sustainable and desired future conditions. The the abundance of recreational fi shes is declining HNA addressed the system-wide, river reach, in La Grange Pool and the Open River Reach and pool level spatial scales, and included the 

87
bluff-to-bluff extent of the fl oodplain. The describe existing habitat conditions, trends, and 

development of the HNA relied heavily on opportunities. The Environmental Pool Plans 

the long-term monitoring data gathered by the are useful communication and planning tools 

LTRMP. The primary purpose of the HNA was that will help guide future habitat rehabilitation 

to help guide selection, design, and evaluation of on the Upper Mississippi River. Environmental 

HREPs. The HNA began to identify the long- Pool Plans have been completed for the Upper 

term habitat requirements at different scales Impounded Reach, and similar plans are under 

and helped redefi ne the focus of future system development for the Lower Impounded Reach 

monitoring and research activities conducted by and the Unimpounded Reach. No formal 

the LTRMP. Finally, the HNA was instrumental Environmental Pool Plans have been developed 

in identifying system goals, objectives, for the Illinois River, however, under Section 

and opportunities for habitat protection, 519 Water Resources Development Act 2000; a 

enhancement, and rehabilitation projects under comprehensive rehabilitation plan for the Illinois 

the authority of the EMP. River Basin was completed in 2006 by the Corps 

of Engineers, Rock Island District. Research Reports

Multiple research papers, articles, and Navigation and Ecosystem Sustainability Program 

reports have been authored that use LTRMP data Reach Planning

to assess UMRS ecological conditions. Topics The Navigation and Ecosystem Sustainability 

covered by these documents include water Program (NESP) was authorized by Congress 

quality, sediment, hydrology, erosion, vegetation, in fall 2007 and is designed to achieve the dual 

fi sheries, macroinvertebrates, wildlife, and purposes of UMRS ecosystem rehabilitation 

the interrelationships between these subjects. and navigation improvements. Environmental 

The U.S. Geological Survey, U.S. Army Corps reach planning is one of 23 initial NESP 

of Engineers, U.S. Fish and Wildlife Service, environmental projects. This effort builds upon 

state natural resource agencies, and universities the Environmental Pool Plans with a primary 

have produced an extensive collection of these focus of developing a pool-scale process 

research products to help stakeholders better that effi ciently coordinates the selection and 

understand and manage UMRS natural resources. sequencing of rehabilitation efforts in the Upper 

Access to LTRMP USGS reports is available Mississippi River Basin. LTRMP information 

at http://www.umesc.usgs.gov/products.html. is being used in this process to identify existing 

A library catalogue containing about conditions and forecast future system conditions. 

5,000 documents relating to the UMRS is This information has helped develop realistic 

available from the UMRCC at http://www. ecological objectives, identify appropriate 

mississippi-river.com/umrcc/catalog.html. rehabilitation actions, and lay out an effi cient 

project sequencing strategy based on opportunity. 3.2.2 Planning and Decision Making This planning also builds upon past efforts to 

develop ecosystem goals and objectives (DeHaan Environmental Pool Plans et al. 2003). Environmental Pool Plans are being 

developed by state and Federal agencies and U.S. Fish and Wildlife Service Comprehensive 

the public to establish common habitat goals Conservation Plan

and objectives for the UMRS. They identify, by The Comprehensive Conservation Plans 

navigation pool, resource issues, rehabilitation (CCP) for the Upper Mississippi River National 

opportunities and constraints, desired future Wildlife and Fish Refuge, the Mark Twain 

conditions, and potential actions to achieve National Wildlife Refuge, and Illinois River 

desired conditions. Along with experience National Wildlife and Fish Refuges Complex was 

gained from past habitat projects, observations developed to provide UMRS refuge managers 

of river managers, biologists, and members of with a 15-year strategy for achieving refuge 

the public, LTRMP information was used to help purposes and contribute to the mission of the 

88
National Wildlife Refuge System. LTRMP specifi c efforts to link LTRMP data and expertise 

data helped support this initiative by providing to design and evaluation of rehabilitation projects 

information about existing ecological conditions throughout the system.

and trends (e.g., land cover change and island HREP Design Handbook loss). Using this and other environmental The HREP Design Manual (USACE 2006b) data, the CCP provides a refuge vision, goals, was developed to share lessons learned from measurable objectives, and outlines strategies for 20 years of designing and building UMRS reaching those objectives. ecosystem rehabilitation projects. Each chapter 

Decision Support System Tools of the handbook is devoted to different habitat 

The vast amount of UMRS data has made project features, such as shoreline protection, 

ecological planning and decision making more backwater dredging, or islands. Each chapter 

complex. Tools are being developed to help also generally follows the same format including 

manage and more easily access, query, and model a discussion of the resource problem, design 

this information. These tools are commonly methodology, case studies, references, and 

referred to as decision support systems (DSSs). lessons learned. LTRMP data (e.g., bathymetry, 

The DSSs allow users to query large UMRS land cover, and water quality) are used in this 

databases and obtain answers in several formats document help describe resources issues, develop 

including text, tables, graphs, and maps. The appropriate project design, and assess project 

more advanced DSSs allow users to perform performance.

statistical and spatial queries and model if-then UMRS Habitat Rehabilitation scenarios with data. Current DSS tools using Several Federal and state agencies and LTRMP data include 

private organizations are making use of LTRMP • Habitat Needs Assessment Geographic data in their rehabilitation efforts on the UMRS. Information System (GIS) Query Tool State natural resource agencies, U.S. Fish and for the UMRS, Wildlife refuges, and The Nature Conservancy • LTRMP Spatial Data Query and are using land cover, water quality, and fi sheries Visualization Tool, information to help plan, construct, and manage • Middle Mississippi River Decision Mississippi and Illinois River fl oodplains, Support System, wetlands, islands, side channels, and backwater • GIS Tools for Conservation Planning. rehabilitation projects. In addition to EMP and

rehabilitation projects, the Corps is also using • Dabbling Duck Models. LTRMP information to support ecosystem For additional information about these and 

rehabilitation occurring as part of the Illinois other UMRS DSS tools, go to River Basin Restoration Program (519) and http://www.umesc.usgs.gov/dss.html. Continuing Authorities Program (Section 1135, 

3.2.3 Ecosystem Rehabilitation and Management 206, 204), and planned as part of NESP.

Environmental Management Program Habitat 3.3 Future Efforts

Rehabilitation and Enhancement Projects 3.3.1 Enhancing Assessment of Status and Land cover data are used for nearly all EMP Trends HREPs. The LTRMP component data (e.g., 

water quality and fi sheries) have been used in a The LTRMP data provide an excellent 

few select response studies, such as Swan Lake, baseline for comparison with both past and 

Peoria, Chautauqua, Pool 8 islands, and Brown’s future data. For each indicator, the data provide 

Lake. When a project is in a Resource Trend information about the status in specifi c years 

Analysis Pool or reach, the data are regularly or seasons, and change among years. The data 

used for resource condition analysis and project have been analyzed to determine both directional 

planning. Since 2007, the LTRMP has engaged in trends over multiple years and patterns and 

89
relations among components, seasons, or within a year typically reduces variability in 

habitats. For systems such as large rivers, which estimates of indicator means making analyses 

exhibit substantial variation both within and more statistically powerful. Thus, for analyses 

among years, 10 years is probably the minimum of relations among components, the amount of 

period needed to provide an acceptable baseline. effort expended within each year is more critical 

A better picture of long-term dynamics, including than for trend analyses. A previous report by 

identifying trends and cycles will develop as Lubinski et al. (2001) assessed the ability to 

more years of data are collected. detect annual change using LTRMP data. Results 

Trends represent responses to longer term from these types of analyses generate hypotheses 

changes in underlying system conditions and specifi c questions that can be evaluated more 

and drivers. For detecting trends, each year rigorously through focused research. 

represents one data point. The ability to detect As currently confi gured, the LTRMP is 

trends will be greatest for indicators that have a broadly based program providing data for 

relatively high levels of underlying change and analyses of both trends and annual change. It 

relatively low levels of variation due to local is diffi cult for any one program to be effi cient 

conditions or sampling methods. This can be at both these types of data collection, but 

illustrated using the LTRMP data on suspended any analysis of change is best achieved when 

solids. In Pool 13, about 90% of the variation consistent and comparable information is 

in summer averages for suspended solids in the provided over time. Changes in the LTRMP 

main channel results from actual year-to-year design or methods that may improve the 

variation rather than from sampling variations or effi ciency of data collection should be 

responses to local conditions. If there were an considered. However, any change should also 

underlying change of 3% per year in suspended consider the existing data and, when possible, try 

solids concentration, it would require about to maintain the continuity of information they 

16 years to detect that trend with statistical power provide. 

of 80%. However, if the underlying annual 3.3.2 Improving Indicator Selection change is 5%, only about 11 years of data are 

required to detect a trend. In both instances, The information presented in this report 

halving or doubling the annual effort for data represents a fi rst attempt to defi ne indicators 

collection would result in only 1 year difference based on LTRMP data. Generally, the most 

to detect the trend. Thus, for detecting trends, useful indicators will be those that relate directly 

the underlying rate of change and the number of to program goals. The more specifi cally those 

years of data are more critical than the amount goals are defi ned, the easier it is to identify an 

of effort expended in each year. For some indicator that relates directly to that goal. The 

indicators, trends may be occurring at rates too goals of the EMP are currently only broadly 

slow to be detected within the 10-year frame defi ned and many of the indicators presented in 

of this report. More information about trend this report were chosen because they can relate 

detection with LTRMP data is available at http:// to these broad perceived goals. Thus, refi ning 

www.umesc.usgs.gov/ltrmp/power_plots.html. and quantifying EMP goals and objectives will 

Annual changes typically represent responses result in the development of more accurate and 

to short-term changes in environmental meaningful indicators.

conditions or interactions among biota. Indicators that change slowly, exhibit high 

Analyses of how annual changes are related variability, or are subject to time lags will 

among different indicators provide hypotheses require many years of information to assess the 

about what might be causing some of the changes underlying trends. Yet those trends are derived 

observed. Yearly differences in factors such from changes in processes and function within 

as fl ows, temperatures, reproductive success the system. Thus, it may also be useful to defi ne 

of biota, and sediment inputs can increase surrogate indicators that identify changes in 

interannual variation in indicators. More effort processes (e.g., nutrient processing, feeding 

90
relations, growth rates) that foreshadow changes rehabilitation and continued monitoring. The 

in abundances. Determining these surrogate next step is to assist the river stakeholders with 

indicators will require further analyses and the creation of an objective, functional evaluation 

focal studies, which will also help contribute system to measure the acceptability of ecological 

to the broader EMP goal of improving our conditions within each reach and clarify what 

understanding of how the UMRS functions. In management actions are the most urgent. This 

addition, for fi shes in particular, further analyses 10-year review of status and trends on the river 

are suggested to compare the usefulness of system provides the fi rst opportunity to renew 

community metrics, representative species, or this process. 

functional guilds as indicators. As river management becomes more 

Endpoints are the values or set of conditions collaborative and adaptive, attention will become 

that defi ne the desired system condition. When more focused on the appropriate scale at which to 

these endpoints are achieved, the management monitor and manage. The LTRMP data indicate 

program has, by defi nition, been successful. the reach level is most appropriate for assessing 

Endpoints can be defi ned using specifi c units of many biota, but that materials, such as sediments 

measurement, level of resolution, desired ranges, and nutrients, may be better served at larger 

degree of statistical certainty, and target dates scales (e.g., system level). Finally, the LTRMP 

that enable quantitative assessment of progress. has aggressively pursued innovative, useful ways 

Indicators should be expressed using the same to serve program data. The Program stands as a 

metrics that apply to endpoints. For most of national leader in developing and implementing 

the current indicators for the UMRS, endpoints a successful multipartner collaboration that 

or target ranges have not yet been determined. transcends traditional geo-political boundaries 

An active process should be used by the EMP that often hamper environmental programs. 

partnership to defi ne and refi ne endpoints as Ultimately, society’s investment in 

understanding of the UMRS is increased. monitoring programs must be justifi ed by the 

relevance and utility of the information the 3.3.3 Conclusions program provides to its users. The relevance 

A well-designed, adaptable monitoring of a monitoring program increases over time, 

system is the fi rst step in documenting efforts as changes in status and trends of important 

toward sustaining and, where possible, improving resources can be more reliably detected and 

the ecological integrity of the UMRS fl oodplain this information can be directly incorporated 

reaches. Historical observations and current into management actions and question-driven 

LTRMP data clearly indicate that the reaches scientifi c investigations. The continuing role of 

have been changed by human activity in ways the LTRMP will be to provide the data needed 

that have diminished the original integrity of the to assess the results of management actions 

river. The scientifi c evidence provided in this and how these changes should be viewed in the 

report from the LTRMP suggests that fl oodplain context of the ecological integrity of the river 

river reaches of the UMRS require further system.

91

References

Anderson, K. B., R. E. Sparks, and A. A. Paparo. on submersed vegetation in an Illinois River 

1978. Rapid assessment of water quality using pool, USA. Aquatic Plant Control Research 

the fi ngernail clam, Musculium transversum. Program Technical Notes Collection (ERDC 

University of Illinois, Water Resources Center, TN-APCRP-EA-07), U.S. Army Engineer 

Urbana, Illinois, U-WRC-78-0133, Research Research and Development Center, Vicksburg, 

Report (133). 115 pp. Mississippi.

Anfi nson, J. O. 2003. The river we have wrought: Best, E. P. H., G. A. Kiker, and W. A. Boyd. 

A history of the Upper Mississippi. University 2004b. A simulation model on the competition 

of Minnesota Press. Minneapolis, Minnesota. for light of meadow-forming and canopy365 pp. forming aquatic macrophytes at high and low 

nutrient availability. Aquatic Plant Control Barko, J. W., M. S. Adams, and N. L. Cleseri. Research Program ERDC/EL TR-04-14, U.S. 1986. Environmental factors and their Army Engineer Research and Development consideration in the management of submersed Center, Vicksburg, Mississippi. aquatic vegetation: a review. Journal of 

Aquatic Plant Management 24:1–10. Bhowmik, N. G., and J. R. Adams. 1989. 

Successional changes in habitat caused Barko, J. W., D. G. Hardin, and M. S. Matthews. by sedimentation in navigation pools. 1982. Growth and morphology of submersed Hydrobiologia 176/177:17–27. macrophytes in relation to light and 

temperature. Canadian Journal of Botony Bhowmik, N. G., T. W. Soong, W. F. Reichelt, 

60:877–887. and N. M. L. Seddik. 1992. Waves generated 

by recreational traffi c on the Upper Barko, V. A., M. W. Palmer, D. P. Herzog, and Mississippi River System. Report by the B. Ickes. 2004. Infl uential environmental Illinois State Water Survey, Champaign, gradients and spatiotemporal patterns of Illinois, for the U.S. Fish and Wildlife Service, fi sh assemblages in the unimpounded Upper Environmental Management Technical Center, Mississippi River. American Midland Onalaska, Wisconsin, in fulfi llment of Project Naturalist 151:369–385. Number FWS14-16-0003-80-973, November 

Belanger, K. D., D. J. Dieterman, and T. W. 1992. EMTC 92-S003. 68 pp. (NTIS PB92-

Deyo. 1990. Pre- and post-construction water 161868)

quality monitoring for habitat rehabilitation Bodensteiner, L. R., and W. M. Lewis. 1992. and evaluation projects at Big Lake Bay, Role of temperature, dissolved oxygen, Finger Lakes, Lake Onalaska, and the Pool 8 and backwaters in the winter survival of Islands area of the Upper Mississippi River. freshwater drum (Aplodinotus grunniens) in U.S. Fish and Wildlife Service Environmental the Mississippi River. Canadian Journal of Management Technical Center. Onalaska, Fisheries and Aquatic Sciences 49:173–184. Wisconsin. EMTC 90–94. 17 pp.

Brauer, E. J., D. R. Busse, C. Strauser, R. D. Bellrose, F. C., F. L. Paveglio, and D. W. Davinroy, D. C. Gordon, J. L. Brown, J. Steffeck. 1979. Waterfowl populations and E. Myers, A. M. Rhoads, and D. Lamm. the changing environment of the Illinois River 2005. Geomorphology study of the middle valley. Illinois Natural History Survey Bulletin Mississippi River. U.S Army Corps of Volume 32, Article 1. Urbana, Illinois. 54 pp. Engineers, St. Louis District, Engineering 

Best, E. P. H., A. H. Teeter, and S. K. Nair. Division, Final Report.

2004a. Modeling the impacts of suspended Carlander, K. D., C. A. Carlson, V. Gooch, and sediment concentration and current velocity T. L. Wenke. 1967. Populations of Hexagenia

93
naiads in Pool 19, Mississippi River, 1959– River-Illinois System environmental 

1963. Ecology 48:873–878. objectives planning workshops, Interim 

Report. Prepared for the U.S. Army Engineer Carlson, D. M. 1992. Importance of wintering District, Rock Island, St. Louis, and St. Paul. refugia to the largemouth bass fi shery in the 37 pp. Hudson River estuary. Journal of Freshwater 

Ecology 7:173–180. Descy, J. P. 1992. Eutrophication in the River 

Meuse. In D. W. Sutcliffe, and J. G. Jones, Chamberlin, F. 1994. Wind-generated waves in editors. Eutrophication: Research and navigation pools. Report by the U.S. Army Application to Water Supply. Freshwater Corps of Engineers, St. Paul, Minnesota, Biological Association. for the National Biological Service, 

Environmental Management Technical Dettmers, J. M., S. Gutreuter, D. H. Wahl, and 

Center, Onalaska, Wisconsin, December 1994. D. A. Soluk. 2001. Patterns in abundance 

LTRMP 94-S001. 16 pp. (NTIS PB95-209532) of fi shes in main channels of the upper 

Mississippi River. Canadian Journal of Chen, Y. H. and D. B. Simmons. 1986. Fisheries and Aquatic Sciences 58:933–942. Hydrology, hydraulics, and geomorphology 

of the Upper Mississippi River System. Dodds, W. K., J. R. Jones, and E. B. Welch. 1998. 

Hydrobiologia 136:5–20. Suggested classifi cation of stream trophic 

state: distributions of temperate stream types Chick, J. H., B. S. Ickes, M. A. Pegg, V. A. by chlorophyll, total nitrogen and phosphorus. Barko, R. A. Hrabik, and D. P. Herzog. 2005. Water Research 32:1455–1462. Spatial structure and temporal variation of fi sh 

communities in the Upper Mississippi River Donner, S. D., C. J. Kucharik, and J. A. Foley. 

System. U.S. Geological Survey, UMESC, 2004. Impact of changing land use practices 

La Crosse, Wisconsin, May 2005. LTRMP on nitrate export by the Mississippi River. 

Technical Report 2005-T004. 15 pp. Global Biogeochemical Cycles 18: Art. No. 

GB1028. Chick, J. H., and M. A. Pegg. 2001. Invasive carp 

in the Mississippi River Basin. Science 292 Eldridge, J. 1988. Aquatic invertebrates 

(5525): 2250–2251. important for waterfowl production. U.S. Fish 

and Wildlife Service, Fish and Wildlife Leafl et Chick, J. H., M. A. Pegg, and T. M. Koel. 2006. 13.3.3, Waterfowl Management Handbook, Spatial patterns of fi sh communities in the 

U.S. Department of the Interior. 6 pp. Upper Mississippi River System: Assessing 

fragmentation by low-head dams. River Engstrom, D. R., J. E. Almendinger, D. W. Kelly, 

Research and Applications 22:413–427. and E. A. Nater. 2000. Historical changes 

in sediment and phosphorus loading to the Cochran, W. G. 1977. Sampling techniques, 3rd Upper Mississippi River: Mass-balance edition. John Wiley and Sons, New York. reconstructions from the sediments of Lake 

Coker, R. E. 1929. Studies of common fi shes Pepin. Final Research Report Prepared for the 

of the Mississippi River at Keokuk. U.S. Metropolitan Council Environmental Services. 

Department of Commerce, Bureau of Minneapolis, Minnesota. 50 pp.

Fisheries, Document 1072. Fischer, J. R., J. N. Houser, K. L. Hoff, and E. 

Cunjak, R. A. 1996. Winter habitat of selected Harms. 2005. Spatial and temporal variation 

stream fi shes and potential impacts from land- of dissolved oxygen. Pages 28–38 in

use activity. Canadian Journal of Fisheries and Houser, J. N., editor. Multiyear synthesis of 

Aquatic Sciences 53(Supplement 1):267–282. limnological data from 1993 to 2001 for the 

DeHaan, H. C., N. M. McVay, C. H. Theiling, Long Term Resource Monitoring Program. 

and R. S. Soileau. 2003. Upper Mississippi U.S. Geological Survey, Upper Midwest 

Environmental Sciences Center, La Crosse, 

94
Wisconsin. LTRMP Technical Report 2005- Gutreuter, S., R. Burkhardt, and K. Lubinski. 

T003. 59 pp. 1995. Long Term Resource Monitoring 

Program procedures: Fish monitoring. Fremling, C. R. 1964. Mayfl y distribution National Biological Service, Environmental indicates water quality on the Upper Management Technical Center, Onalaska, Mississippi River. Science 146:1164–1166. Wisconsin, July 1995. LTRMP 95-P002-1. 

Fremling, C. R. 1989. Hexagenia mayfl ies: 42 pp. + Appendixes A–J.

Biological monitors of water quality in the Gutreuter, S., A. D. Bartels, K. Irons, and M. B. Upper Mississippi River. Journal Minnesota Sandheinrich. 1999. Evaluation of the fl ood- Academy of Science 55:139–143. pulse concept based on statistical models 

Fremling, C.R. 2005. Immortal river: The Upper of growth of selected fi shes of the Upper 

Mississippi in ancient and modern times. Mississippi River System. Canadian Journal of 

University of Wisconsin Press. Madison, Fisheries and Aquatic Sciences 56:2282-2291.

Wisconsin. 429 pp. Gutreuter, S., J. M. Dettmers, and D. H. Wahl. 

Fremling, C. R., J. L. Rasmussen, R. E. Sparks, 2003. Estimating mortality rates of adult fi shes 

S. P. Cobb, C. F. Bryan, and T. O. Clafl in. from entrainment through the propellers of 

1989. Mississippi River fi sheries: a case river towboats. Transactions of the American 

history. Pages 309–351 in D. P. Dodge, editor. Fisheries Society 132:646–661.

Proceedings of the International Large River Hoopes, D. T. 1960. Utilization of mayfl ies Symposium, Honey Harbour, Ontario, Canada, and caddisfl ies by some Mississippi River Canadian Special Publication of Fisheries and fi shes. Transactions of the American Fisheries Aquatic Sciences. Society 89:32–34.

Goolsby, D. A., and W. A. Battaglin. 2001. Long- Houser, J. N., editor. 2005. Multiyear synthesis term changes in concentrations and fl ux of of limnological data from 1993 to 2001 for nitrogen in the Mississippi River Basin, USA. the Long Term Resource Monitoring Program. Hydrological Processes 15:1209–1226. Final report submitted to the U.S. Army Corps 

Gray, B. R., R. J. Haro, J. T. Rogala, and J. of Engineers from the U.S. Geological Survey, 

S. Sauer. 2005. Modeling fi ngernail clam Upper Midwest Environment Sciences Center, 

(Family: Sphaeriidae) abundance-habitat La Crosse, Wisconsin, March 2005. LTRMP 

associations at two spatial scales using Technical Report 2005-T003. 59 pp. (NTIS 

hierarchical count models. Journal of PB2005-105228) 

Freshwater Biology 50: 715–729. Hughes, R. M., D. P. Larsen, and J. M. Omernik. 

Green, W. E. 1984. The great river refuge. Pages 1986. Regional reference sites: A method for 

431–439 in A. S. Hawkins, R. C. Hanson, assessing stream potentials. Environmental 

H. K. Nelson, and H. M. Reeves, editors. Management 10:629–635.

Flyways: pioneering waterfowl management Ickes, B. S. 2005. A research framework for in North America. Supplement of documents, aquatic over-wintering issues in the Upper U.S. Government Printing Offi ce, Washington Mississippi River Basin. U.S. Geological D. C., May 1984. Survey, Upper Midwest Environmental 

Grumbine, R. E. 1994. What is ecosystem Sciences Center, La Crosse, Wisconsin. 26 pp. 

management? Conservation Biology. 8:27–38. + Appendixes A–B.

Gutreuter, S. 2004. Challenging the assumption Ickes, B. S., M. C. Bowler, A. D. Bartels, D. J. 

of habitat limitation: An example from Kirby, S. DeLain, J. H. Chick, V. A. Barko, 

centrarchid fi shes over an intermediate spatial K. S. Irons, and M. A. Pegg. 2005. Multiyear 

scale. River Research and Applications synthesis of the fi sh component from 1993 to 

20:413–425. 2002 for the Long Term Resource Monitoring 

95
Program. U.S. Geological Survey, Upper Knox, J. C. and D. J. Faulkner. 1994. PostMidwest Environmental Sciences Center, La settlement erosion in the lower Buffalo River 

Crosse, Wisconsin. LTRMP 2005-T005. 60 pp. watershed. Final report to the Western District, 

+ CD-ROM (Appendixes A–E). Wisconsin Department of Natural Resources, 

Eau Claire, Wisconsin. 83 pp. Johnson, J. H. 1976. Effects of tow traffi c on the 

resuspension of sediments and on dissolved Koel, T. M. 2001. Classifi cation of Upper 

oxygen concentration in the Illinois and Mississippi River pools based on contiguous 

Upper Mississippi Rivers under normal pool aquatic/geomorphic habitats. Journal of 

conditions. Technical Report Y-76-1. U.S. Freshwater Ecology, 16:159–170.

Army Corps of Engineers. St. Louis, Missouri. Koel, T. M. 2004. Spatial variation in fi sh 129 pp. species richness of the upper Mississippi 

Johnson, M. G., and W. H. Charlton. 1960. Some River system. Transactions of the American 

effects of temperature on the metabolism and Fisheries Society 133:984–1003.

activity of largemouth bass. Progressive Fish- Korschgen, C. E. 1990. Feasibility study: Culturist 22:155–163. Impacts of turbidity on growth and production 

Johnston, D. K., and P. W. Aasen. 1989. The of submersed plants. Report by the U.S. Fish 

metropolitan wastewater treatment plant and and Wildlife Service, Northern Prairie Wildlife 

the Mississippi River: 50 years of improving Research Center, La Crosse, Wisconsin, 

water quality. Journal of the Minnesota for the U.S. Fish and Wildlife Service, 

Academy of Science. 55(1):134–138. Environmental Management Technical Center, 

Onalaska, Wisconsin, November 1990. EMTC Jude, D. J. 1968. Bottom fauna utilization and 90-07. 11 pp. (NTIS PB91135475) distribution of ten species of fi sh in Pool 19, 

Mississippi River. M.S. Thesis, Iowa State Kreiger, K. A., D. W. Schloesser, B. A. 

University, Ames. 238 pp. Manny, C. E. Trisler, S. E. Heady, J. H. 

Ciborowski, and K. N. Muth. 1996. Evidence Knight, S. K., and T. M. Parchure. 2004. of the recovery of burrowing mayfl ies Hydraulic effects of recreation boat traffi c on (Ephemeroptera: Ephemeridae: Hexagenia) the Upper Mississippi River System, Vol. 1. in western Lake Erie. Journal of Great Lakes ENV Report 3. U.S. Army Corps of Engineer Research 22:254– 263. Research and Devlopment Center, Vicksburg, 

Mississippi. 91 pp. Kreiling, R. M., Y. Yin, and D.T. Gerber. 

2007. Abiotic infl uences on the biomass of Knox, J. 2000. Geomorphic reaches of the Vallisneria americana Michx. in the Upper Upper Mississippi River System. Chapter 5 Mississippi River: River Research and in: WEST Consultants Inc. 2000. Volume 1. Applications, 23:343–349. Geomorphic Assessment. Upper Mississippi 

River and Illinois Waterway cumulative effects Kundzewicz, Z. W., L. J. Mata, N. W. Arnell, 

study. Report prepared for the U.S. Army P. Döll, P. Kabat, B. Jiménez, K. A. Miller, 

Corps of Engineers, Rock Island District, T. Oki, Z. Sen, and I. A. Shiklomanov. 2007. 

Rock Island, Illinois. Freshwater resources and their management. 

Climate change 2007: Impacts, adaptation and Knox, J. C., P. J. Bartlein, K. K. Hirschboeck, vulnerability. Contribution of Working Group and R. J. Muckenhirn. 1975. The response of II to the Fourth Assessment Report of the fl oods and sediment yields to climate variation Intergovernmental Panel on Climate Change, and land use in the Upper Mississippi M. L. Parry, O. F. Canziani, J. P. Palutikof, P. Valley. University of Wisconsin, Institute for J. van der Linden and C. E. Hanson, editors, Environmental Studies Report No. 52. 76 pp. Cambridge University Press, Cambridge, UK, 

173–210.

96
Kushlan, J. A. 1978. Feeding ecology of wading McCabe, G. J., and D. M. Wolock. 2002. A step 

birds. Pages 249–297 in A. Sprunt, IV, J. C. increase in streamfl ow in the conterminous 

Ogden, and S. Winckler, editors. Wading birds. United States. Geophysical Research Letters 

National Audubon Society Research Report 29(24), 2185, doi:10.1029/2002GL015999, 

No. 7, National Audubon Society, New York. 2002.

Landwehr, K. J., C. H. Theiling, T. R. Gambucci, Meade, R. W., editor. 1995. Contaminants in the 

D. R. Busse, J. M. Stemler, D. B. Wilcox. Mississippi River, 1987–92. U.S. Geological 

2005. Water level management opportunities Survey Circular 1133, Reston, Virginia. 140 

for ecosystem restoration on the Upper pp.

Mississippi River and Illinois Waterway. Mills, B. H., W. C. Starett, and F. C. Bellrose. U.S. Army Corps of Engineers, Rock 1966. Man’s effect on the fi sh and wildlife Island District, Rock Island, Illinois. Upper of the Illinois River. Illinois Natural History Mississippi River- Illinois Waterway System Survey Biological Notes No. 57. Urbana, Navigation Study ENV Report 53. 139 pp. Illinois. 24 pp.

Langrehr, H. A., B. R. Gray, and J. A. Janvrin. Mitsch, W. J., J. W. Day, Jr., J. W. Gilliam, P. 2007. Evaluation of aquatic macrophyte M. Groffman, D. L. Hey, G. W. Randall, and community response to island construction N. Wang. 2001. Reducing nitrogen loading in the Upper Mississippi River. Lake and to the Gulf of Mexico from the Mississippi Reservoir Management 23:313–320. River Basin: Strategies to counter a persistent 

Lubinski, K. S., and J. W. Barko. 2003. Upper ecological problem. BioScience 51:373–388.

Mississippi River System Navigation Myslinski, E., and W. Ginsburg. 1977. and Ecosystem Sustainability Program: Macroinvertebrates as indicators of pollution. Environmental Science Panel Report. U.S. American Water Works Association Journal Army Corps of Engineers, Env Report 52. 69:538–544.

Lubinski, K, R. Burkhardt, J. Sauer, D. Soballe, Nelson, J. C., A. Redmond, and R. E. Sparks. and Y. Yin. 2001. Initial analyses of change 1994. Impacts of settlement on fl oodplain detection capabilities and data redundancies vegetation at the confl uence of the Illinois and in the Long Term Resource Monitoring Mississippi Rivers. Transactions of the Illinois Program. U.S. Geological Survey, Upper State Academy of Science 87(3&4):117–133. Midwest Environmental Sciences Center, La 

Crosse, Wisconsin, September 2001. LTRMP Patrick, P. 1998. Rivers of the United States, 

2001-T001. 23 pp. + Appendixes A-E. (NTIS Vol. IV. Part A: the Mississippi River and 

PB2002-100123) tributaries north of St. Louis. John Wiley & 

Sons, Inc., New York. 408 pp. Lubinski, K. S., and S. Gutrueter 1994. 

Ecological information and habitat Pegg, M. A., and M. A. McClelland. 2004. 

rehabilitation on the Upper Mississippi River. Spatial and temporal patterns in fi sh 

Pages 87–100 in L. W. Hesse, C. B. Stalnaker, communities along the Illinois River. Ecology 

N. G. Benson, and J. R. Zuboy, editors. 1994. of Freshwater Fish 13:125–135.

Proceedings of the Symposium, Restoration Pinter, N. 2005a. Policy forum: Floodplain Planning for the Rivers of the Mississippi encroachment since the 1993 fl ood. Science 

River Ecosystem, National Biological Survey, 308:207–208.

Washington, D.C. Biological Report 19. 

Reprinted by the National Biological Survey, Pinter, N. 2005b. One step forward, two steps 

Environmental Management Technical back on U.S. fl oodplains, Science 308:201–

Center, Onalaska, Wisconsin. December 1994. 208.

LTRMP 94-R010. 14 pp. 

97
Pinter, N., B. S. Ickes, J. H. Wlosinski, and R. of Fisheries and Aquatic Sciences 61:1102–

van der Ploeg. 2006. Trends in fl ood stages: 1112.

Contrasting results from the Mississippi and Rogala, J. T., J. H. Wlosinski, and K. J. Rhine River systems. Journal of Hydrology Landwehr. 1999. Pool 13 drawdown: 331: 554–566. Predicting success rates and affected areas. 

Pinter, N., and R. Thomas, 2003. Engineering U.S. Geological Survey, Upper Midwest 

modifi cations and changes in fl ood behavior Environmental Sciences Center, La Crosse, 

of the Middle Mississippi River. Pages 96–114 Wisconsin, April 1999. LTRMP 99-T002. 

in R. Criss and D. Wilson, editors. At the 27 pp. + Appendix. (NTIS PB99-145393) 

confl uence: Rivers, fl oods, and water quality Rogala, J. T., P. J. Boma, and B. R. Gray. 2003. in the St. Louis Region. Rates and patterns of net sedimentation 

Pinter, N., R. Thomas, and J. H. Wlosinski. 2001. in backwaters of Pools 4, 8, and 13 of the 

Assessing fl ood hazard on dynamic rivers. Upper Mississippi River. U.S. Geological 

Transactions of the American Geophysical Survey, Upper Midwest Environmental 

Union 82:333,338–339. Sciences Center, La Crosse, Wisconsin. An 

LTRMP Web-based report available online Rabalais, N. N., R. E. Turner, and D. Scavia. at http://www.umesc.usgs.gov/data_library/ 2002. Beyond science into policy: Gulf of sedimentation/documents/rates_patterns/ Mexico hypoxia and the Mississippi River. page1.html. BioScience 52:129–142.

Rogers, S., T. Blackburn, H. Langrehr, J. Nelson, Raibley, P. T., K. S. Irons, T. M. O’Hara, K. and A. Spink. 1998. 1994 annual monitoring D. Blodgett, and R. E. Sparks. 1997. Winter at selected locations in Pools 4, 8, 13, and 26 habitats used by largemouth bass in the Illinois and La Grange Pool of the Upper Mississippi River, a large river-fl oodplain ecosystem. River System. U.S. Geological Survey, North American Journal of Fisheries Environmental Management Technical Center, Management 15:390–399. Onalask, Wisconsin, July 1998, LTRMP 98-

Ranthum, R. G. 1969. Distribution and food P009, 22 pp. + Appendixes A–B 

habits of several species of fi sh in Pool 19, Rosenberg, D. M., and V. H. Resh. 1993. Mississippi River. M.S. Thesis, Iowa State Freshwater biomonitoring and benthic University, Ames. 207 pp. macroinvertebrates. Chapman and Hall, New 

Richardson, L. A. H., and T. L. Clemment. 1993. York. 488 pp.

A summary of water quality characteristics Sandusky, M. J., and R. E. Sparks. 1979. at selected habitat sites in Navigation Pool Investigations of declines in fi ngernail clam 8 of the Mississippi River from July 17, (Musculium transversum) populations in the 1988, to December 31, 1990. Report by the Illinois River and Pool 19 of the Mississippi Wisconsin Department of Natural Resources, River. The Bulletin of the American Onalaska, Wisconsin, for the U.S. Fish and Malacological Union, Inc. 1979:11–15. Wildlife Service, Environmental Management 

Technical Center, Onalaska, Wisconsin, June Sauer, J. 2004. Multiyear synthesis of the 

1993. EMTC 93-S009. 21 pp. (NTIS PB94- macroinvertebrate component from 1992 to 

108255). 2002 for the Long Term Resource Monitoring 

Program. U.S. Geological Survey, Upper Richardson, W. B., E. A. Strauss, L. A. Bartsch, Midwest Environment Sciences Center, La E. M. Monroe, J. C. Cavanaugh, L. Vingum, Crosse, Wisconsin, Technical Report LTRMP and D. M. Soballe. 2004. Denitrifi cation in the 2004-T005. 31 pp. + Appendixes A–C. Upper Mississippi River: Rates, controls, and 

contribution to nitrate fl ux. Canadian Journal Sheehan, R. J., P. S. Wills, M. A. Schmidt, and J. 

E. Hennessy. 2004. Determinations of the fate 

98
of fi sh displaced from low-velocity habitats Sparks, R. 1992. The Illinois River-Floodplain 

at low temperatures. U.S. Army Corps of ecosystem. Pages 412–432 in National 

Engineers, Upper Mississippi River- Illinois Research Council (U.S.) Committee on 

Waterway System Navigation Study, ENV Restoration of Aquatic Ecosystems: Science, 

Report 32, Rock Island, Illinois. 11 pp. Technology, and Public Policy (editors). 

Restoration of Aquatic Ecosystems. National Simon, T. P. 1999. Assessing the sustainability Academy of Sciences, USA. and biological integrity of water resources 

using fi sh communities. CRC Press, Boca Sparks, R. E. 1995. Need for esosystem 

Roton, Florida. 671 pp. management of large rivers and their 

fl oodplains. Bioscience 45:168–182. Simons, D. B., S. A. Schumm, and M. A. 

Stevens. 1974. Geomorphology of the Sparks, R. E., J. C. Nelson, and Y. Yin. 1998. 

Middle Mississippi River. Report DACW39- Naturalization of the fl ood regime in regulated 

73-C-0026, U.S. Army Corps of Engineers, St. rivers. BioScience 48:706–720.

Louis District, St. Louis, Missouri. 110 pp. Starrett, W. C. 1972. Man and the Illinois 

Smith, R. A., R. B. Alexander, and G. E. River. Pages 131–167 in R. T. Oglesby, C. 

Schwarz. 2003. Natural background A. Carlson, and J. A. McCann, eds. River 

concentrations of nutrients in streams and Ecology and Man. Academic Press, New York. 

rivers of the coterminous United States. 465 pp.

Environmental Science and Technology Steingraber, M. T., and J. G. Wiener. 1995. 37:3039–3047. Bioassessment of contaminant transport and 

Smith, V. H., B. G. Tilman, and J. C. Nekola. distribution in aquatic ecosystems by chemical 

1999. Eutrophication: impacts of excess analysis of burrowing mayfl ies (Hexagenia). 

nutrient inputs on freshwater, marine, and Regulated Rivers: Research & Management 

terrestrial ecosystems. Environmental 11:201–209.

Pollution 100:179–196. Stoddard J. L., D. P. Larsen, C. P. Hawkins, R. 

Soballe, D. M., and J. R. Fischer. 2004. K. Johnson, and R. H. Norris. 2006. Setting 

Long Term Resource Monitoring Program expectations for the ecological condition of 

procedures: Water quality monitoring. streams: the concept of reference condition. 

U.S. Geological Survey, Upper Midwest Ecological Applications 16:1267–1276.

Environmental Sciences Center, La Crosse, Strauss, E. A., W. B. Richardson, L. A., Bartsch, Wisconsin, March 2004. Technical Report J. C. Cavanaugh, D. A. Bruesewitz, H. LTRMP 2004-T002-1 (Ref. 95-P002-5). 73 pp. Imker, J. A Heinz, and D.M. Soballe. 2004. + Appendixes A–J. Nitrifi cation in the Upper Mississippi River: 

Sparks, R. E. 1980. Response of fi ngernail clam patterns, controls, and contribution to the 

populations in the Keokuk Pool (Pool 19) NO3- budget. Journal of the North American 

to the 1976–1977 drought. Pages 43–71 in Benthological Society 23:1–14.

J. L. Rasmussen, editor. Proceedings of the The Nature Conservancy. 1998. Illinois River site UMRCC symposium on the Upper Mississippi conservation plan. The Nature Conservancy River bivalve mollusks. Rock Island, Illinois. of Illinois. Illinois Project Offi ce, Lewiston, 

Sparks, R. E. 1984. The role of contaminants Illinois. 

in the decline of the Illinois River: The Wetlands Initiative. 1997. Farming the Implications for the Mississippi: Pages fl oodplain. The potential for fl ood tolerant 25–66 in J. G. Wiener, R. V. Anderson, and fl oodplain uses. Proceedings of a workshop, D. R. McConville, editors. Contaminants in Moline, Illinois, September 1997. 66 pp + the Upper Mississippi River. Butterworth attachments. Publishers, Stoneham, Massachusetts. 

99
Thiel, P. A., and J. S. Sauer. 1999. Long Minnesota. Available online at www.umrba.

Term Resource Monitoring Program org/wq/wq2002rpt.pdf.

Procedures: Macroinvertebrate monitoring. Upper Mississippi River Conservation U.S. Geological Survey, Upper Midwest Committee (UMRCC). 2000. A river that Environmental Sciences Center, La Crosse, works and a working river. Upper Mississippi Wisconsin, Revised May 1999. LTRMP 95- River Conservation Committee. Rock Island, P002-2 (Revised 1999). 7 pp + Appendixes Illinois. 36 pp. A–H.

Upper Mississippi River Conservation Theiling, C. H. 1995. Habitat rehabilitation on Committee (UMRCC). 2003. Proposed water the upper Mississippi River: Regulated Rivers quality criteria necessary to sustain submersed Research & Management 11:227–238. aquatic vegetation in the Upper Mississippi 

Theiling, C. H., C. Korschgen, H. DeHaan, T. River. Upper Mississippi River Conservation 

Fox, J. Rohweder, and L. Robinson. 2000. Committee. Rock Island, Illinois. 6 pp. 

Habitat needs assessment for the Upper U.S. Army Corps of Engineers (USACE). 2000. Mississippi River System: Technical Report. Upper Mississippi River System Habitat U.S. Geological Survey, Upper Midwest Needs Assessment: Summary report 2000. Environmental Sciences Center, La Crosse, U.S. Army Corps of Engineers, St. Louis Wisconsin. Contract report prepared for the District, St. Louis, Missouri. 53 pp. U.S. Army Corps of Engineers, St. Louis 

District, St. Louis, Missouri. 248 pp + U.S. Army Corps of Engineers (USACE). 2004. 

Appendixes A to AA. Upper Mississippi River-Illinois Waterway 

System navigation feasibility study, feasibility Thompson, D. 1973. Feeding ecology of diving report. Rock Island District, St. Paul District, ducks on Keokuk Pool, Mississippi River. and St. Louis District. Journal of Wildlife Management 37:367–381.

U.S. Army Corps of Engineers (USACE). 2006a. Tucker, J. K., C. H. Theiling, K. D. Blodgett, Illinois River Basin restoration conprehensive and P. A. Thiel. 1993. Initial occurrences of plan. U.S. Army Corps of Engineers, Rock zebra mussels (Dreissena polymorpha) on Island District, Rock Island, Illinois. 551 pp. freshwater mussels (Family Unionidae) in the 

Upper Mississippi River System. Journal of U.S. Army Corps of Engineers (USACE). 

Freshwater Ecology 8(3):245–251. 2006b. Upper Mississippi River System, 

Environmental Management Program, Turner, R. E., and N. N. Rabalais. 2003. Linking Environmental Design Handbook. U.S. Army landscape and water quality in the Mississippi Corps of Engineers, Rock Island District, River Basin for 200 years. BioScience Rock Island, Illinois. 462 pp. 53:563–572.

U.S. Environmental Protection Agency (USEPA). Tyson, J. T. and R. L. Knight. 2001. Response 2000a. Nutrient criteria: Technical guidance of yellow perch to changes in the benthic manual: Rivers and Streams. EPA 822B-00- invertebrate community of western Lake 002. Washington, D.C. Erie. Transactions of the American Fisheries 

Society 130:766–782. U.S. Environmental Protection Agency 

(USEPA). 2000b. Progress in water quality: Upper Mississippi River Basin Association An evaluation of the national investment (UMRBA). 2004. Upper Mississippi River in municipal wastewater treatment. EPA- water quality: The states approaches to 832-R-00-008. U.S. Environmental Protection Clean Water Act monitoring, assessment, Agency. Washington, D.C. Available online and impairment decisions. Upper Mississippi at http://www.epa.gov/owmitnet/wquality/ River Basin Association Report. St. Paul, benefi ts.html. 

100
U.S. Fish and Wildlife Service (USFWS). 2006. fi ngernail clam Musculium transversum in 

Comprehensive conservation plan for the the Upper Mississippi River. Hydrobiologia 

Upper Mississippi River National Wildlife and 304:209–220.

Fish Refuge. U.S. Fish and Wildlife Service. Wlosinski, J. 1999. Hydrology. Pages 6-1 to 228 pp. 6-10 in U.S. Geological Survey. Ecological 

U.S. Geological Survey (USGS). 1997. status and trends of the Upper Mississippi 

Annual work plan, fi scal year 1997, for River System 1998: A report of the Long 

the Upper Mississippi River System Long Term Resource Monitoring Program. 

Term Resource Monitoring Program. USGS U.S. Geological Survey, Upper Midwest 

Environmental Management Technical Center. Environmental Sciences Center, La Crosse, 

Onalaska, Wisconsin. LTRMP 1997-P005. 67 Wisconsin. LTRMP 99-T001. 236 pp. 

pp + Appendixes A–D. Yin Y. and H. A. Langrehr. 2005. Multiyear 

U.S. Geological Survey (USGS). 1999. synthesis of the aquatic vegetation 

Ecological status and trends of the Upper component from 1991 to 2002 for the 

Mississippi River System 1998: A report of Long Term Resource Monitoring Program. 

the Long Term Resource Monitoring Program. U.S. Geological Survey, Upper Midwest 

U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, 

Environmental Sciences Center, La Crosse, Wisconsin. Technical Report LTRMP 2005-

Wisconsin. LTRMP 99-T001. 236 pp. T001. 29 pp. + Appendixes A–F.

Wasley, D. 2000. Concentration and movement Yin, Y., and J. C. Nelson. 1995. Modifi cations to 

of nitrogen and other materials in selected the Upper Mississippi River and their effects 

reaches and tributaries of the Upper on fl oodplain forests. National Biological 

Mississippi River System. M.S. Thesis. Service, Environmental Management 

University of Wisconsin, La Crosse, Technical Center, Onalaska, Wisconsin, 

Wisconsin. February 1995. LTRMP 95-T003. 17 pp. 

(NTIS PB95-201208). Welch, E. B., J. M. Jacoby, and C. W. May. 

1998. Stream quality. In R. J. Naiman and Yin, Y, J. C. Nelson, and K. S. Lubinski. 1997. 

R. E. Bilby, editors. River Ecology and Bottomland hardwood forests along the Upper 

Management. Springer. New York. Mississippi River. Natural Areas Journal 

17:164–173. WEST Consultants, Inc. 2000. Final report: 

Upper Mississippi River and Illinois Yin, Y., J. S. Winkelman, and H. A. Langrehr. 

Waterway cumulative effects study, Volume 1: 2000. Long Term Resource Monitoring 

Geomorphic Assessment. ENV Report 40-1. Program procedures: Aquatic vegetation 

228 pp. monitoring. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, La Wilcox, D. B., E. L. Stefanik, D. E. Kelner, M. Crosse, Wisconsin. April 2000. LTRMP 95- A. Cornish, D. J. Johnson, I. J. Hodgins, S. J. P002-7. 8 pp. + Appendixes A–C. Zigler, and B. L. Johnson. 2004. Improving 

fi sh passage through navigation dams on the 

Upper Mississippi River System. Interim 

report of the Upper Mississippi River- Illinois 

Waterway System navigation study, U.S. Army 

Corps of Engineers, Rock Island District. ENV 

Report 54. 110 pp + Appendixes A–D.

Wilson, D. M., T. J. Naimo, J. G. Wiener, R. 

V. Anderson, M. B. Sandheinrich, and R. E. 

Sparks. 1995. Declining populations of the 

101

Appendix A

Glossary of terms used in this report

adaptive management: An approach to natural used to refer to areas that feed into dams; may 

resources management that acknowledges the also refer to areas served by a sewerage or 

risk and uncertainty of ecosystem restoration stormwater system.

and allows for modifi cation of restoration channel training structure: A human-made measures to optimize performance. The process fl ow obstruction (e.g., wing dam, closing dam, or of implementing policy decisions as scientifi cally revetment) used to divert river fl ow to a desired driven management experiments that test location, usually toward the center of the main predictions and assumptions in management channel to increase fl ow and limit sedimentation plans, and using the resulting information to or to protect the riverbank from eroding. improve the plans. A mechanism for integrating 

scientifi c knowledge and experience for the community: A grouping of populations of 

purpose of understanding and managing natural different species found living together in a 

systems. Adaptive management is a continuous, particular environment.

iterative process by which the consequences conservation: Active management to ensure the of management actions and policies are survival of the maximum diversity of species, systematically evaluated, and the actions and and the maintenance of genetic diversity within policies modifi ed in response to the resulting new species; implies the maintenance of ecosystem information. functions; embraces the concept of long-term 

backwater: Small, generally shallow body of sustainability; a careful preservation and 

water attached to the main channel, with little protection of something; especially planned 

or no current of its own; shallow, slow-moving management of a natural resource to prevent 

water associated with a river but outside the exploitation, destruction, or neglect.

river’s main channel. corridor: A relatively narrow strip of habitat 

basin: The entire geographical area drained by a that crosses an area of nonhabitat land and serves 

river and its tributaries, such as the Illinois River to connect larger areas of habitat.

basin. desired future conditions: A description 

bathymetry: The measurement of water depth of management goals for an area to achieve 

across a water body. optimal conditions; the descriptions should 

be constructed with the input of all interested benthic: Refers to the bottom layer of any body parties in the region and should include clear of water and the organisms therein. goals for species, communities, and ecosystem 

biodiversity: The variety of living organisms composition, structure, and functions across the 

considered at all levels of organization, from landscape. For this system study, the desired 

genetics through species, to higher taxonomic future condition was based on coordination 

levels, and including the variety of habitats and with resource managers and became the system 

ecosystems, as well as the process occurring objectives.

therein. Biodiversity occurs at four levels: drawdown: Lowering the level of water in a genetic diversity, species richness, ecosystem selected portion of an aquatic system; conducted diversity, and landscape diversity. for habitat management purposes with dams or 

biotic: Living; as applied to the components of pumps. 

an ecosystem. ecological (or biological) integrity: A system’s 

catchment: Watershed; the area drained by a wholeness or “health,” including presence of 

stream, lake, or other body of water. Frequently all appropriate elements, biotic and abiotic, and 

103
occurrence of all processes that generate and fertile soils, genetic variation, clean water, and 

maintain those elements at the appropriate rates. clean air.

The capability of supporting and maintaining ecosystem sustainability: The ability of aquatic, a balanced, integrated, adaptive community wetland, and terrestrial complexes to maintain of organisms having a species composition, themselves as self-regulating, functioning diversity, and a functional organization systems. comparable to that of natural, unimpacted habitat 

of the region. fi sh passage: Modifi cation or removal of 

human-made barriers that would otherwise 

ecosystem: Dynamic and interrelating complex restrict or prevent movement or migration of fi sh. of plant and animal communities and their 

associated nonliving environment; a biological fl oodplain: Lowlands bordering a river that 

community together with the physical and are subject to fl ooding, thereby providing fl ood 

chemical environment with which it interacts. storage. Floodplains are composed of sediments 

carried by rivers and deposited on land during ecosystem function: Processes that drive the fl ooding and contain a mosaic of habitat types. ecosystem; any performance attribute or rate 

function at some level of biological organization geomorphology: The science that deals with 

(e.g., energy fl ow, sedimentation, detritus land and submerged relief features (landforms) of 

processing, nutrient spiraling). the earth’s surface; the physical structure of the 

river fl oodplain environment. ecosystem health: A condition when a system’s 

inherent potential is realized, its condition habitat: The living place of an organism or 

is stable, its capacity for self-repair, when community, characterized by its physical or 

perturbed, is preserved, and minimal external biotic properties; habitats can be described on 

support for management is needed. many scales from microhabitat to ecosystems to 

biomes.

ecosystem management: Protecting, conserving 

or restoring the function, structure, and species hydrologic: Pertaining to the cyclic phenomena 

composition of an ecosystem, recognizing that all of waters of the earth; successively as 

components are interrelated. precipitation, runoff, storage and evaporation, 

and quantitatively as to distribution and ecosystem or ecological processes: The concentration. aggregate of all interactions among the various 

biotic components of an ecosystem (e.g., hydrology: A science dealing with the 

migration, pollination, predation), between the properties, distribution, and circulation of 

abiotic and biotic components of an ecosystem water on the surface of the land, in the soil and 

(e.g., nutrient uptake, erosion, respiration) and underlying rocks, and in the atmosphere.

natural events and cycles (e.g., fi re regimes, hypoxia: The condition in which dissolved 

hydrologic cycles) that operate over different oxygen concentrations are less than two parts scales of time and space. per million of water (e.g., zones in the Gulf of 

ecosystem restoration: Management actions Mexico and other estuaries).

that attempt to accomplish a return of natural impoundment: The volume of standing water areas or ecosystems to a close approximation of that is maintained behind a dam.

their conditions prior to human disturbance, or to 

less degraded, more natural conditions in terms indicator: A measurable surrogate for 

of structure and function. environmental endpoints, such as biodiversity, 

that are assumed to be of value to the public; ecosystem services: All of the goods and are sensitive to changes in the environment; and services provided to humanity by natural can warn that environmental changes are taking ecosystems; examples include wood products, place.

104
invasive species: Any species that has the point source pollution: pollution into bodies 

tendency to invade or enter a new location or of water from specifi c discharge points, such as 

niche; an introduced species that out competes sewer outfalls or industrial-waste pipes.

native species for space and resources; an alien pool: The area of water that is impounded and species whose introduction does or is likely to maintained at a higher level behind a navigation cause economic or environmental harm or harm dam; generally refers to the length of river to human health. between sequential dams.

landscape: A heterogeneous land area composed population: A group of individuals of the same of interacting ecosystems that are repeated species occupying an area small enough to permit in similar form throughout; landscapes are interbreeding among all members of the group. variable in size; usually overlaps governmental 

jurisdictions, thus requiring collaboration from a prairie: An area of land of low topographic 

broad range of participants. relief that principally supports grasses and 

herbs, with few trees, and is generally of a mesic levee district: Cooperative quasi-governmental (moderate) climate. Most of the Great Plains; organizations that protect areas from fl oodwaters, most of Ohio, Indiana, Illinois, and Iowa; and primarily for agricultural areas, but may also much of Missouri and Minnesota is considered serve as wildlife areas. prairie. Almost all of this area has been converted 

life history: An organism’s patterns of growth, into farmland. Fire is an important part of prairie 

reproduction, and longevity that are related to ecology; naturally occurring and human-induced 

specifi c demands for survival in a particular place fi res were common in prairie areas. Grazing by 

at a particular time. animals, such as the American bison and prairie 

dogs, also helped maintain the original prairie macroinvertebrates: Small, but visible with environment. the naked eye, animals without backbones 

(insects, worms, larvae, etc). Water bodies have reach: A continuous stretch or expanse. In 

communities of aquatic macroinvertebrates. reference to rivers, it can be used to defi ne 

The species composition, species diversity and portions of rivers at different scales (i.e., pool 

abundance of the macroinvertebrates in a given reach, reach between two river bends).

water body can provide valuable information reference condition: The range of factors (e.g., on the relative health and water quality of a hydrology, sediment movement, animal and waterway. plant communities, and channel geometry) that 

management action: A structural or non- is representative of an area or ecosystem prior to 

structural measure that modifi es or adjusts the signifi cant alteration of its environment.

condition of the ecosystem. rehabilitation: Improvements to a natural 

moist soil unit: An area where water levels are resource; putting back into good condition or 

controlled to provide a desired mix of moist soil working order. 

vegetation, generally for use by waterfowl. restoration: Reestablishing degraded ecosystem 

nonnative species: Species of plants and structure, function, and dynamic processes to 

animals that are imported or unintentionally a less degraded, more natural condition. In its 

transported to a new location where they do not broadest usage, restoration encompasses the 

naturally occur. following concepts: conservation, enhancement, 

naturalization, preservation, protection, nonpoint source pollution: Water pollution rehabilitation, restoration, and stabilization. produced by diffuse watershed land-use 

activities. riparian: Areas that are contiguous to and 

affected by surface and subsurface hydrologic 

features of perennial or intermittent water bodies 

105
(e.g., rivers, streams, lakes, or drainage ways); structure: The horizontal and vertical spatial 

pertaining to the boundary between water and arrangement, or confi guration, of a habitat, 

land; normally represents the streamside zone community or ecosystem; includes biotic and 

and the area of infl uence of the stream. abiotic diversity.

river stage: The elevation of the water surface succession: Sequential change in the vegetation 

(usually in feet) above an arbitrary datum. at a particular location over time. 

savanna: Area with a well-developed sustainable/sustainability: A level and method 

herbaceous ground cover composed principally of resource use that does not destroy the health 

of prairie species with scattered trees at densities and integrity of the systems that provide the 

ranging form 1 per acre to roughly 50% canopy resource; thus the long-term resource availability 

closures. The frequency of fi re maintains this does not diminish due to such use. 

habitat type by infl uencing the amount and temporal: Of, relating to, or limited by time. density of woody vegetation encroaching into the 

prairie environment. threatened and endangered species: Those 

species that are listed as threatened or endangered sediment resuspension: The movement of under the Federal Endangered Species Act (ESA) sediment from the river bed into the water of 1973, and those species that are candidates or column due to a disturbance (e.g., wave action). proposed as candidates for listing under the ESA; 

sediment transport: The movement of sediment listing can occur at the Federal or state level or 

(usually by water). both.

sedimentation: The process of sediment being tributary: A stream or river whose water fl ows 

deposited in a given location. into a larger stream or river.

side channel: Aquatic channel connected to turbidity: Measure of the “lack of clearness” 

the main channel and separated from the main of water; an expression of the optical property 

channel by an island; usually has fl owing water. that causes light to be scattered and absorbed 

rather than transmitted in straight lines through a species: One or more populations of individuals sample; the measure of relative sample clarity. that can interbreed, but cannot successfully breed 

with other organisms. watershed: The geographic area that naturally 

drains into a given watercourse, such as a stream species diversity: The richness, abundance, or river. and variability of plant and animal species and 

communities.

species richness: A simple count of the number 

of species in an area.

stakeholder: Those organizations and/or 

individuals having a vested interest in the 

outcome of a decision making process.

stressor: A substance or action that has the 

potential to cause an adverse effect on an 

ecosystem.

106
Appendix B

Acronyms used in this report

CCP Comprehensive Conservation Plan TN Total Nitrogen

CPUE Catch Per Unit Effort TP Total Phosphorus

DO Dissolved Oxygen TSS Total Suspended Solids

DSS Decision Support System UMESC Upper Midwest Environmental 

EMP Environmental Management Sciences Center

Program UMR Upper Mississippi River

GIS Geographic Information System UMRCC Upper Mississippi River 

HNA Habitat Needs Assessment Conservation Committee

HREP Habitat Rehabilitation and UMRS Upper Mississippi River System

Enhancement Project USACE U.S. Army Corps of Engineers

IWW Illinois Waterway USEPA U.S. Environmental Protection 

LTRMP Long Term Resource Monitoring Agency

Program USFWS U.S. Fish and Wildlife Service

NESP Navigation and Ecosystem USGS U.S. Geological Survey 

Sustainability

107

Form Approved REPORT DOCUMENTATION PAGE OMB No. 0704-0188

Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, 

searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments 

regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the 

Offi ce of Management and Budget, Paperwork Reduction Project (0704-0188), Washington, D.C. 20503

1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE 3. REPORT TYPE AND DATES COVERED

November 2008

4. TITLE AND SUBTITLE 5. FUNDING NUMBERS

Status and trends of selected resources of the Upper Mississippi River System

6. AUTHOR(S)

B. L. Johnson1 and K. H. Hagerty2, editors

7. PERFORMING ORGANIZATION NAME AND ADDRESS 8. PERFORMING ORGANIZATION

1

U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, REPORT NUMBER

La Crosse, Wisconsin 54603

2 2008-T002 U.S. Army Corps of Engineers, Rock Island District, Clock Tower Building, Rock Island, Illinois 

61204

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSORING/MONITORING

U.S. Geological Survey AGENCY REPORT NUMBER

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

11. SUPPLEMENTARY NOTES

12a. DISTRIBUTION/AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE

Release unlimited. Available from National Technical Information Service, 5285 Port Royal Road, Springfi eld, VA 22161 (1-800-553-6847 or 703-487-4650. Available to registered users from the Defense Technical Information Center, Attn: Help Desk, 8725 Kingman Road, Suite 0944, Fort Belvoir, VA 22060-6218 

(1-800-225-3842 or 703-767-9050).

13. ABSTRACT (Maximum 200 words)

Like other large rivers, the Upper Mississippi River System (UMRS) serves a diversity of roles. The UMRS provides commercial 

and recreational fi shing, fl oodplain agriculture, drinking water for many communities, an important bird migration pathway, a variety of 

recreational activities, and a navigation system that transports much of the country’s agricultural exports. These multiple roles present 

signifi cant management challenges. 

14. SUBJECT TERMS 15. NUMBER OF PAGES

Drivers, ecosystem, fi sh, Illinois River, indicators, integrity, macroinvertebrates, nutrients, sediment, stressors, 

sustainability, Upper Mississippi River, vegetation 102 pp. + Appendixes A–B 

16. PRICE CODE

17. SECURITY CLASSIFICATION 18. SECURITY CLASSIFICA- 19. SECURITY CLASSIFICA- 20. LIMITATION OF ABSTRACT

 OF REPORT TION TION

 OF THIS PAGE OF ABSTRACT

Unclassifi ed

Unclassifi ed Unclassifi ed


Long Term Resource Monitoring Program - Status and Trends of Selected Resources of the Upper Mississippi River System

The Long Term Resource Monitoring Program (LTRMP) for the Upper Mississippi 

River System was authorized under the Water Resources Development Act of 1986 as 

an element of the Environmental Management Program. The mission of the LTRMP 

is to provide river managers with information for maintaining the Upper Mississippi 

River System as a sustainable large river ecosystem given its multiple-use character. 

The LTRMP is a cooperative effort by the U.S. Geological Survey, the U.S. Army 

Corps of Engineers, and the States of Illinois, Iowa, Minnesota, Missouri, and 

Wisconsin.