Long Term Resource Monitoring Program

 Technical Report 

2005-T001

January 2005

Multiyear Synthesis of the Aquatic Vegetation Component 

from 1991 to 2002

for the Long Term Resource Monitoring Program 
Long Term Resource Monitoring Program Technical Reports

provide Long Term Resource Monitoring Program 

partners with scientific and technical support.

All reports in this series receive anonymous peer review.

Cover graphic by Mi Ae Lipe-Butterbrodt

Mention of trade names or commercial products does not constitute endorsement

or recommendation for use by the U.S. Department of the Interior, U.S. Geological Survey.
Multiyear Synthesis of the Aquatic Vegetation Component 

from 1991 to 2002 

for the Long Term Resource Monitoring Program

by

Yao Yin and Heidi Langrehr

Final Report submitted to

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

Clock Tower Building

PO Box 2004

Rock Island, Illinois 61204-2004

January 2005

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603
Suggested citation:

Yin Y. and H. A. Langrehr. Multiyear Synthesis of the Aquatic Vegetation Component from 1991 to 2002 for the Long Term 

Resource Monitoring Program. U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin. 

LTRMP 2005 T001. 29 pp. + Appendixes A–F. 

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

Springfield, 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

Preface ......................................................................................................... vii

Chapter 1: Introduction .................................................................................... 1

Chapter 2: Status and Trends .............................................................................. 7

Methods ................................................................................................ 7

Transect Sampling Protocol ..................................................................... 7

Stratified Random Sampling Protocol ......................................................... 8

Data Analysis .................................................................................... 8

Results ................................................................................................... 9

Distribution Patterns .............................................................................. 9

Temporal Dynamics .............................................................................. 13

Chapter 3: Outpool Sampling .............................................................................. 18

Methods ................................................................................................ 18

Results ................................................................................................... 18

Chapter 4: Environmental Factors ........................................................................ 20

Methods ................................................................................................ 20

Results ................................................................................................... 20

Chapter 5: Habitat Rehabilitation and Enhancement Project .......................................... 22

Methods ................................................................................................ 22

Results ................................................................................................... 22

Chapter 6: Summary ....................................................................................... 26

Acknowledgments .......................................................................................... 27

References ................................................................................................... 27

Appendix A. Total Number of Points Sampled Along Transects by Pool and Year, 

1991–2002 ....................................................................................... A-1

Appendix B. Percent Frequency of Occurrence of Submersed Aquatic Vegetation by Year, 

Sampling Strata, and Pool for Stratified Random Sampling 1998–2002, Long Term

Resource Monitoring Program, Upper Mississippi River System ........................ B-1

Appendix C. Percent Frequency of Occurrence by Species for Pools 4, 5, and 7 Based on 

2002 Stratified Random Sampling, Long Term Resource Monitoring Program, 

Upper Mississippi River System ............................................................... C-1

Appendix D. Percent Frequency of Occurrence by Species for Pool 11 in 2001 and Pools 8, 

12, and 13 Based on 2002 Stratified Random Sampling, Long Term Resource 

Monitoring Program, Upper Mississippi River System .................................... D-1

Appendix E. Percent Frequency of Occurrence by Species for Pool 26 and Alton Pool Based 

on 2002 Stratified Random Sampling, Long Term Resource Monitoring Program, 

Upper Mississippi River System ............................................................... E-1

Appendix F. Percent Frequency of Occurrence by Species for La Grange Pool Based on 

2002 Stratified Random Sampling, Long Term Resource Monitoring Program, 

Upper Mississippi River System ............................................................... F-1

Page
iv

Tables

1.1. Sampling area acres, number of sites sampled, and field days per year of the transect 

sampling versus the stratified random sampling (SRS) .................................... 6

2.1. Percent frequency of occurrence for aquatic vegetation collected during stratified random 

sampling in upper and lower Pool 4, Pools 5, 7, 8, 11, 12, 13, and 26 of the Upper 

Mississippi River and Alton and La Grange Pools fo the Illinois River, Long Term 

Resource Monitoring Program from 1998 to 2002 .......................................... 12

4.1. Long Term Resource Monitoring Program water quality sites and U.S. Army Corps of 

Engineers gage station by pool .................................................................. 21

4.2. Results from an analysis of variance to determine the effects of turbidity and water level 

elevation on the percent frequency of submersed aquatic vegetation, Long Term 

Resource Monitoring Program, Upper Mississippi River System ........................ 21

4.3. Results from an analysis of variance to determine the effects of turbidity, water level elevation,

and river mile on the percent frequency of submersed aquatic vegetation, Long Term 

Resource Monitoring Program, Upper Mississippi River System ........................ 21

5.1. Abundance index by species outside the Stoddard Bay Habitat Rehabilitation and 

Enhancement Project area of Pool 8, Upper Mississippi River System .................. 24

5.2. Abundance index by species inside the Stoddard Bay Habitat Rehabilitation and Enhancement 

Project area of Pool 8, Upper Mississippi River System .................................... 24

Number
v

Figures

1.1. Upper Mississippi River System pool sampled for aquatic vegetation, Long Term Resource

Monitoring Program .............................................................................. 2

1.2. Location and arrangement of transects in Pool 4, Upper Mississippi River System ......... 3

1.3. Location and arrangement of transects in Pool 8, Upper Mississippi River System ......... 3

1.4. Location and arrangement of transects in Pool 13, Upper Mississippi River System ......... 4

1.5. Location and arrangement of transects in Alton Pool, Illinois River ........................... 4

1.6. Location and arrangement of transects in La Grange Pool, Illinois River ..................... 5

2.1. Presence of submersed aquatic vegetation in a section of Pool 8, Upper Mississippi River 

System on the basis of 1998 to 2002 data pooled together ................................. 10

2.2. Presence of submersed aquatic vegetation in Pool 8, Upper Mississippi River System on the 

basis of 1998 to 2002 data pooled together ................................................... 11

2.3. Mean total suspended solids in main channel and backwater strata in Long Term Resource 

Monitoring Program key pools during summer stratified sampling from 1993 through

2001 ................................................................................................ 13

2.4. Presence of selected submersed aquatic species in Pool 13, Upper Mississippi River System,

from 1998 to 2002 ................................................................................. 14

2.5. Percent frequency of submersed aquatic species from different sampling efforts by year in 

upper Pool 4 (above river mile 775), Upper Mississippi River System .................. 14

2.6. Percent frequency of submersed aquatic species from different sampling efforts by year in 

lower Pool 4 (below river mile 775), Upper Mississippi River System .................. 15

2.7. Percent frequency of submersed aquatic species from different sampling efforts by year in 

Pool 8, Upper Mississippi River System ...................................................... 15

2.8. Percent frequency of submersed aquatic species from different sampling efforts by year in 

Pool 13, Upper Mississippi River System ...................................................... 16

2.9. Percent frequency of submersed aquatic species from different sampling efforts by year in 

Pool 26, Upper Mississippi River System, and the lower 12 miles of Alton Pool, 

Illinois River ....................................................................................... 17

2.10. Percent frequency of submersed aquatic species from different sampling efforts by year in 

La Grange Pool, Illinois River .................................................................. 17

3.1. Detrended correspondence analysis (ordination) of study areas based on frequency of 

occurrence of all aquatic species from 1998 to 2002 ....................................... 19

3.2. Correlation between percent frequency of submersed aquatic vegetation and two 

environmental factors, mean water turbidity and water level fluctuations, by pool ...... 19

5.1. Treatment and control area in the impounded area near Stoddard, Wisconsin, in Pool 8, 

Upper Mississippi River System ............................................................... 23

5.2. Abundance index for submersed, rooted floating-leaf, and emergent aquatic vegetation in the

Stoddard Bay Habitat Rehabilitation and Enhancement Project and control area, 

Upper Mississippi River System ............................................................... 25

5.3. Abundance index of American wildcelery, coontail, and Canadian waterweed and percent 

cover of American lotus in the Stoddard Bay Habitat Rehabilitation and Enhancement 

Project area, control area, and Pool 8, Upper Mississippi river System. .................. 25

Number Page
vii

Preface

This report summarizes monitoring activities of the aquatic vegetation component of the Long 

Term Resources Monitoring Program (LTRMP) of the Upper Mississippi River System (UMRS) 

from 1991 to 2002. The LTRMP was authorized under the Water Resources Development Act 

of 1986 (Public Law 99 662) as an element of the U.S. Army Corps of Engineers Environmental 

Management Program. The LTRMP is implemented by the Upper Midwest Environmental Sciences 

Center, a U.S. Geological Survey science center, in cooperation with the five Upper Mississippi River 

System (UMRS) states of Illinois, Iowa, Minnesota, Missouri, and Wisconsin. The U.S. Army Corps 

of Engineers provides guidance and has overall program responsibility. The mode of operation and 

respective roles of the agencies are outlined in a 1988 Memorandum of Agreement. 

The UMRS encompasses the commercially navigable reaches of the Upper Mississippi River, as 

well as the Illinois River and navigable portions of the Kaskaskia, Black, St. Croix, and Minnesota 

Rivers. Congress has declared the UMRS to be both a nationally significant ecosystem and a nationally 

significant commercial navigation system. The mission of the LTRMP is to provide decision makers 

with information for maintaining the UMRS as a sustainable large river ecosystem, given its multiuse 

character. The long term goals of the program are to understand the system, determine resource trends 

and effects, develop management alternatives, manage information, and develop useful products.

This report is to provide a 12-year summary of data regarding the status and trends of aquatic 

vegetation within the UMRS. In this report we present the results of both transect surveys (conducted 

between 1991 and 2000) and stratified random sampling surveys (conducted between 1998 and 2002) 

of the aquatic vegetation resources of the UMRS and provide an assessment of the effects of a Habitat 

Restoration and Enhancement Project in Pool 8. Work was performed by field station personnel 

from Minnesota, Wisconsin, Iowa, Illinois, and Missouri under the direction of staff from the Upper 

Midwest Environmental Sciences Center. This document satisfies Task 2.2.4 under Goal 2, Monitor 

Resource Change of the Operating Plan (U.S. Fish and Wildlife Service 1993). This document was 

developed with funding provided by the Long Term Resource Monitoring Program.
Multiyear Synthesis of the Aquatic Vegetation Component 

from 1991 to 2002 

for the Long Term Resource Monitoring Program

by

Yao Yin

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

2630 Fanta Reed Road, La Crosse, Wisconsin 54603

and

Heidi Langrehr

Wisconsin Department of Natural Resources LTRMP Onalaska Field Station

 2630 Fanta Reed Road, La Crosse, Wisconsin 54603

Abstract: Aquatic vegetation data were collected in the Upper Mississippi River System (UMRS) under the Long Term 

Resource Monitoring Program (LTRMP). From 1991 to 2002, five reaches were surveyed every year (key pools), and another 

five reaches were surveyed once (outpools). The study design changed from a protocol involving sampling along transects 

(1991–2000) to a protocol incorporating stratified random sampling (1998–2002) with concurrent sampling under both protocols 

in 1998–2000. The frequency of occurrence of plants revealed no synchronous trends among three key pools (Pools 4, 8, and 

13) supporting sizable submersed aquatic vegetation beds. Submersed aquatic vegetation in upper Pool 4 declined steadily 

between 1991 and 2002. Submersed aquatic vegetation in lower Pool 4 declined between 1991 and 1996 and thereafter recovered 

moderately. Submersed aquatic vegetation in Pool 8 increased between 1991 and 1999, which probably was a recovery process 

from a reported sudden collapse after the 1987–1989 drought. Submersed aquatic vegetation in Pool 13 demonstrated a high 

degree of stability during the period of monitoring despite drastic fluctuations between spring and summer sampling in some 

years. Water turbidity and water level fluctuation were strongly correlated with the longitudinal pattern of submersed aquatic 

vegetation distribution in the UMRS. Pools with clearer water and less fluctuating water levels supported more submersed 

aquatic vegetation. The LTRMP key pools represented a wide spectrum of the UMRS habitats. The habitat rehabilitation and 

enhancement project (HREP) at Stoddard Bay in Pool 8 effectively stimulated colonization by aquatic vegetation. 

Key words: Aquatic vegetation, rooted floating-leaf, Illinois River, key pools, Long Term Resource Monitoring Program, Upper 

Mississippi River, outpools, submersed vegetation 

Chapter 1: Introduction

Aquatic vegetation refers to plants with leaves 

and stems growing above, on, or under the 

surface of the water and are usually anchored to 

the sediments by their roots. Aquatic vegetation 

in the Upper Mississippi River System (UMRS; 

Figure 1.1) is desirable because of its many values, 

most notably as food for migratory waterfowl 

(Korschgen et al. 1988) and habitat for fish. 

The construction of a series of locks and dams 

in the 1930s in the Upper Mississippi River 

(UMR) to create a 9-foot deep navigation channel 

also created vast shallow backwaters ideal for 

aquatic vegetation. Growth of aquatic vegetation 

was categorized as excellent inside the Upper 

Mississippi Wildlife and Fish Refuge (Pools 4 

through 14) for three decades before symptoms 

of deterioration associated with permanent 

impoundment became apparent (Green 1984). 

A widespread and sudden decline of American 

wildcelery (Vallisneria americana Michx.) in Pools 

5 through 19 during the late 1980s and early 1990s 

elevated the concern that the UMR might be on the 

verge of a drastic degradation as occurred in the 

Illinois River (Rogers and Theiling 1998).
2

The Illinois River harbored abundant aquatic 

vegetation in its expansive backwaters until 

the early twentieth century (Mills et al. 1966; 

Bellrose et al. 1979). The completion of the 

Chicago Sanitary and Ship Canal in 1900 

diverted water from Lake Michigan and sewage 

from Chicago down the Illinois River and raised 

the water levels several feet causing a decline in 

aquatic vegetation. Aquatic vegetation increased 

in the late 1920s and early 1930s because of the 

construction of many sewage treatment plants 

along the river and a reduction in the amount of 

water diverted from Lake Michigan in 1939. A 

collapse of vegetation abundance and fingernail 

clam populations in the mid-1950s were 

important indicators of ecological degradation of 

the Illinois River (Sparks 1984). 

Vegetation sampling was first included in 

the Long Term Resource Monitoring Program 

(LTRMP) in 1989. Terrestrial and aquatic plant 

communities encountered along transect lines 

laid across the entire width of the floodplain 

in Pools 8, 13, and 26 of the UMR 

were quantified and mapped. In 1990, 

additional transects were established in 

Pool 4 of the UMR and La Grange Pool 

of the Illinois River. In all five pools, 

quadrats were selected for quantitative 

sampling at 50-meter intervals along 

each transect and data on species 

present were collected (Langrehr 1992; 

Peitzmeier-Romano et al. 1992; Shay 

and Gent 1992). 

In 1991, a programmatic decision 

was made to focus on submersed 

aquatic vegetation (SAV) for three 

major reasons. First, SAV was the 

most dynamic plant life form in the 

UMR. Second, SAV was of greatest 

concern to river managers because of 

a recent decline, and third, data on the 

vegetation above the water surface 

(emergent and rooted floatingleaf 

species) were collected using aerial 

photography. The primary objective 

of sampling along transects was to 

describe status and trends of submersed 

aquatic vegetation in selected 

backwaters (Figures 1.2–1.6; Appendix 

A) in Pools 4, 8, 13, and 26 and the La 

Grange Pool (Rogers et al. 1998), although data 

on the presence of rooted floating-leaf vegetation 

were also recorded. The Open River reach, below 

St Louis, Missouri, was not sampled because 

it consisted of large channels not supporting 

sizable and stable submersed aquatic vegetation 

beds. Vegetation was sampled along transects 

once in spring and once in summer (Rogers and 

Owens 1995). Sampling locations (boat stops) 

along transects were spaced at either 15- or 

30-m intervals. Lengths of transects varied by 

location. In general, sampling along a transect 

was terminated when the water depth at sampling 

locations exceeded 2.5 m for an extended 

distance (e.g., into open water). However, 

in situations where the distance across open 

water to areas of SAV was minimal, sampling 

continued until either depth again increased 

beyond 2.5 m for an extended distance or a 

shoreline was reached. Transect sampling of 

selected backwaters continued through 2000.

Figure 1.1. Upper Mississippi River System pool sampled for aquatic vegetation, 

Long Term Resource Monitoring Program.
3

Figure 1.3. Location and arrangement of transects in Pool 8, Upper 

Mississippi River.

Figure 1.2. Location and arrangement of transects in Pool 4, Upper Mississippi River.
4

Figure 1.4. Location and arrangement of transects in Pool 13, Upper Mississippi River.

Figure 1.5. Location and arrangement of transects in Alton Pool, Illinois River.
5

Figure 1.6. Location and arrangement of transects in La Grange Pool, Illinois River.

In 1998, a stratified random sampling (SRS) 

protocol was begun (Yin et al. 2000b) to collect 

data from all shallow water areas where SAV 

could potentially exist. The transect sampling 

was then discontinued after three concurrent 

sampling seasons with the SRS protocol. The 

LTRMP Onalaska Field Station (Wisconsin 

Department of Natural Resources) received a 

grant from the U.S. Environmental Protection 

Agency funding one additional season of transect 

sampling in Pool 8. From 1998 to 2002, SRS was 

conducted annually in Pools 4, 8, 13, and 26 of 

the UMR and in the lower 12 miles of the Alton 

Pool and entire La Grange Pool of the Illinois 

River (Figure 1.1). Other reaches were sampled 

once during the same period to evaluate the 

longitudinal heterogeneity of aquatic vegetation 

outside the key pools (hereafter referred to as 

“outpool” sampling as opposed to “key” pool 

sampling). These included Pool 11 in 2001 

and Pools 5, 7, and 12 and upper Alton Pool 

(excluding the lower 12 miles) in 2002 (Table 1). 

We analyzed the transect protocol data and 

the SRS protocol data for information that 

would improve our understanding of the UMRS 

ecosystem and shed light on the pros and cons of 

environmental engineering for habitat restoration. 

The main body of this report consists of chapters 

addressing four separate topics. The status and 

trends of submersed aquatic vegetation in the 

key pools are evaluated in Chapter 2. Similarities 

between key pools and outpools are compared 

in Chapter 3 to examine the longitudinal 

heterogeneity of the UMRS. The environmental 

factors correlated with the longitudinal patterns 

and temporal dynamics of aquatic vegetation 

in the UMRS are identified in Chapter 4. The 

effectiveness of an environmental engineering 

project (HREP) to promote aquatic vegetation 

growth in Pool 8 is examined in Chapter 5. Each 

chapter consists of introduction, methods, and 

results sections. Conclusions are drawn at the end 

of the report in Chapter 6. 
6

Table 1.1. Sampling area acres, number of sites sampled, and field days per year of the transect sampling versus the 

stratified random sampling (SRS). 

Acres Number of sites sampled per year 

(average ± standard deviation)

Field days per year (average 

± standard deviation)

Sampling area Transect SRS Transect SRS Transect SRS

Pool 4 3,236 80,946 1,743 ± 86 600 ± 50 29 ±4 27 ± 4

Pool 8 873 70,514 2,468 ± 215 621 ± 50 33 ± 4 24 ± 1

Pool 13 1,527 77,224 1,653 ± 148 572 ± 24 31 ± 6 26 ± 3

Pool 26a 669 55,245 878 ± 319 467 ± 129 9 ± 3 28 ± 5

La Grange Pool 287 76,128 325 ± 78 462 ± 55 14 ± 3 29 ± 1 a

Includes the lower 12 miles of the Alton Pool of the Illinois River
7

Chapter 2: Status and Trends

The 9-foot navigation channel developed 

in the Upper Mississippi River during the 

early twentieth century altered the river’s 

geomorphology and flow regimes (Belt 1975; 

Simons et al 1975; Scarpino 1985; Grubaugh 

and Anderson 1989), and consequently brought 

about major changes in the river’s plant 

communities. Terrestrial species were extirpated 

on newly inundated areas and aquatic species 

took their place (Yeager 1949, Green 1960). 

Water smartweeds (Polygonum spp.) were the 

dominant plants during the first 5 years. Soon 

after, smartweeds were replaced by assemblages 

of pondweeds (Potamogeton spp.), coontail 

(Ceratophyllum demersum L.), water stargrass 

(Heteranthera dubia [Jacq.] MacM.), and 

American wildcelery (Vallisneria americana 

Michx.; Green 1960; Rogers and Theiling 1998). 

Since the early 1960s, American wildcelery 

has become the most common species in the 

impounded areas of Pools 4–14 (Rogers 1994; 

Rogers and Theiling 1998). 

The 9-foot navigation channel has undoubtedly 

changed the ecological function of the UMR 

in many ways, most of which have yet to be 

revealed and understood. One way, for example, 

is an observed shift of waterfowl migration 

routes toward the UMR in the 1960s and 1970s 

concurrent with the proliferation of American 

wildcelery in the UMR and deterioration of this 

important food source elsewhere (Korschgen et 

al. 1988; Korschgen and Green 1988). Aerial 

photos collected over the past six decades reveal 

a steady eroding of islands in the impounded 

areas of Pool 8 and a subsequent retreat of 

SAV (Fischer and Claflin 1995). Following a 

basin-wide drought (1987–89), SAV in many 

pools of the UMR declined rapidly within a few 

years (Rogers 1994; Fischer and Claflin 1995). 

Many biologists were concerned that the UMR 

was following the footsteps of the Illinois River 

where SAV collapsed during the 1950s and has 

not yet recovered. When aquatic vegetation 

monitoring under the LTRMP was initiated in 

1991, establishing a reference point and detecting 

trends in terms of frequency of occurrence was 

a top priority identified by river managers. A 

central question was whether the decline of SAV 

observed in the aftermath of the drought was 

continuing.

Methods

Data presented in this chapter were restricted 

to those collected from 1991 to 2000 using the 

transect sampling protocol (Rogers and Owens 

1995) and those collected from 1998 to 2002 

using a stratified random sampling protocol 

(SRS; Yin et al. 2000b). 

Transect Sampling Protocol

In 1991, transects were placed in selected 

backwaters in a nonrandom fashion and sites 

were sampled at either 15 or 30m intervals 

along each transect (Figures 1.2–1.6). Aquatic 

vegetation was sampled once in spring and 

once in summer. Generally, spring sampling 

was between May 15 and June 15 and summer 

sampling was between July 15 and August 31. 

The method used to sample aquatic vegetation 

at each site was modified from a technique used 

by Jessen and Lound (1962). A 2-m diameter 

sampling area was located immediately in front 

of the bow of the sampling boat. The sampling 

area was divided into thirds and plants were 

collected in each third using a long-handled 

thatching rake. The rake was lowered to the 

bottom, twisted 180 degrees to snag vegetation, 

and retrieved. Submersed plant species collected 

on the rake were identified and recorded. After 

all three thirds were sampled; each species 

present was assigned a rating of 1, 2, or 3 on 

the basis of the number of retrievals. A rating of 

4 was assigned to signal high abundance if the 

biomass filled the rake on all three retrievals. 

Beginning in 1997, a rating of “9” was recorded 

to indicate the species was observed in the 

sampling area but not retrieved on the rake. 

Previously, species observed but not retrieved 

were not recorded other than as occasional notes 

in the comment column. If a rooted floating-leaf 

species was present, its vegetative percent cover 

in the sampling area was recorded as follows: 1 

= 1–25% cover, 2 = 26–50% cover, 3 = 51–75% 

cover, and 4 = 76–100% cover. 
8

Stratified Random Sampling Protocol

The stratified random sampling protocol (Yin 

et al. 2000b) was developed to expand the spatial 

coverage of aquatic vegetation sampling from 

limited focal backwaters to the entire aquatic area 

where SAV could potentially exist, to randomize 

the location of sampling sites, and to enhance 

the precision of our estimates. The new sampling 

protocol was initiated to provide pool-wide, 

unbiased, and precise estimates for indices of 

abundance for submersed aquatic vegetation in 

the key pools.

Shallow aquatic areas where SAV could 

potentially exist were mapped using bathymetric 

data collected under the LTRMP. The maximum 

depth for sampling was 3 m in 1998, but 

following an analysis of the data collected, 

the maximum depth was reduced to 2.5 m in 

subsequent years. Shallow water areas were then 

classified into five general habitat types (strata): 

main channel borders, secondary channels, 

contiguous backwaters, isolated backwaters, and 

impounded areas. Allocation of sample sizes 

among strata was initially based on acreage 

and perceived habitat heterogeneity. The initial 

allocation was adjusted in subsequent years 

on the basis of power analysis (90% power for 

detecting 20% of annual pool-wide changes) 

as well as other factors including the water 

level drawdown experiment in Pool 8 during 

2001 and 2002, outpool sampling, and funding 

fluctuations. Sampling locations were selected 

using a random number generator. Site selections 

among years were independent except that the 

2001 sites in Pool 8 were revisited in 2002 to 

track changes occurring at individual sites. The 

revisit of 2001 sites in 2002 should not have had 

materially adverse effects on the estimation of 

stratum-wide or pool-wide means. 

A site was sampled in six areas distributed 

in a cluster surrounding the boat: four off the 

corners and two off the left and right sides. 

Aquatic vegetation was collected from the 

six subsampling areas using a long-handled 

double-headed rake made by welding two 

square-headed garden rakes together. The teeth 

were divided and marked into five equal parts 

(or 20% increments). The rake was extended 

out 1.5 m, lowered to the sediment, and dragged 

back to the boat to snag vegetation. Individual 

species and different life forms of aquatic 

vegetation were recorded as either present or 

absent on the basis of a visual examination and 

their presence in a rake sample. When present, 

submersed species and filamentous algae were 

given a density rating based on their thickness 

on the rake teeth, whereas, rooted floating-leaf 

and emergent species were given a percent cover 

rating on the basis of a visual estimation. 

Data Analysis

The presence or absence of species at each 

site was used to calculate the percent frequency 

of occurrence in each stratum and in all strata 

combined. The percent frequency of occurrence 

is an index of prevalence. For example, SAV was 

recorded at 89 of the 170 sites sampled in the 

contiguous backwater areas of Pool 13 in 1998, 

therefore, its percent frequency of occurrence 

was calculated as 

where y = percent frequency of occurrence, 

a = number of times a species was present, 

n = number of sites sampled, and, where 

the variance of frequency of occurrence was 

calculated as

 15 170

2 * (100 ) 52*(100 52)

     n

y y 

s

where y = percent frequency of occurrence and 

n = number of sites sampled. 

If the study area consisted of several substudy 

areas or stratum investigated separately, the 

percent frequency of occurrence of the study 

area pooled y � � and its variance ( ) 2

pooled �s y � were 

estimated using the formulas for stratified 

random sampling design (Cochran 1977; 

Gutreuter 1997); 

  

   l

1

l

1

h h N

h

y h h N

pooled y

 and

100 52

170

89  *100  *  na

y
9

 



 

 



















l

h h

n

h

s

h N

h

n h N

h N l

h h N pooled s y 1

2 2

1

1 ( ) 2

,

where h

y and 

2

h

s are percent frequency of 

occurrence and its variance, respectively, in 

stratum h; Nh is the acreage of stratum h in terms 

of the number of sampling units; and nh is the 

number of units of Nh investigated.

Pool 4 was split into upper and lower sections, 

divided by a line through Lake Pepin at river 

mile 775 because the two sections displayed 

distinctively different vegetation dynamics. The 

lower 12 miles of the Illinois River, sampled 

along with Pool 26, UMR, was treated as a 

separate pool in analysis because it represents a 

different river. Because the transect and SRS data 

differ in spatial coverage as well as by sampling 

method, we did not expect them to result in 

similar estimates. However, we hoped their 

trends were similar. 

Results

Distribution Patterns

Water clarity and current velocity are two major 

physical variables regulating the distribution 

of SAV in slow-flowing North American 

rivers (Chamber et al. 1991; Vis et al. 2003). 

In the UMR, SAV is affected by many factors, 

including water clarity and current velocity. The 

distribution is complex yet some general patterns 

are revealed by the LTRMP data. The UMR is 

a large, braided floodplain river with extensive 

backwaters of various degrees of connectivity 

to the main channel. A typical cross section of 

the river consists of a few hydrogeomorphic 

features, including the main channel where 

commercial navigation occurs, the main channel 

borders, side channels, contiguous backwaters 

connected to the river year-round, and isolated 

backwaters connected to the river only during 

floods. The frequency of occurrence of SAV 

was highest in isolated backwaters, followed by 

contiguous backwaters, side channels, and main 

channel border in decreasing order (Figure 2.1; 

Appendix B). Such a gradient indicates that 

increased connectivity to the main channel has 

a net negative influence on SAV. The farther 

away and therefore less influenced by the main 

channel, the better the chance for SAV to grow. 

Average current velocity, average water depth, 

and average wind fetch (distance to the nearest 

land mass weighted by the direction and duration 

of winds during a year) displayed a similar 

gradient (Figure 2.1). 

Another hydrogeomorphic gradient exists 

within a navigation pool. The tailwater below 

the upstream dam is most similar to the natural 

river whereas the impounded area above the 

downstream dam is least similar to the natural 

river. The deeper and faster flow in the upper 

section of the pool is a major limiting factor to 

SAV relative to the shallower and slower flow 

in the mid- and lower sections (Figure 2.2). The 

mid- and lower sections have about the same 

average depth. The lower section, however, has 

slightly slower current (28 versus 34 cm/s) but 

much higher effective wind fetch (2,510 versus 

1,220 m) than the midsection. The positive 

influence of slower current is cancelled by the 

negative influence of higher effective wind fetch. 

As a result, the two sections have about the 

same level of SAV presence. These within-pool 

patterns are consistent with historical accounts 

that the establishment of the locks and dams 

navigation system has vastly increased the extent 

of SAV in the UMR because of the creation of an 

expansive shallow impoundment area. 

Across the UMR System (UMRS), SAV was 

widespread in lower Pool 4, Pools 5, 7, 8, and 

13, and rare in Pool 26 and Alton and La Grange 

Pools (Table 2.1). Submersed aquatic vegetation 

was common to infrequent in upper Pool 4 and 

Pools 11 and 12. Lake Pepin, Pool 4, acted as a 

sink for suspended solids (Figure 2.3) improving 

the water clarity in the lower part of the pool 

(J. Houser, USGS-UMESC, unpublished data). 

This, in part, accounted for the difference in the 

amount of SAV between upper and lower Pool 4. 

Factors behind the system-wide distribution 

pattern are described in Chapter 3. 

Dominant SAV species in Pools 4, 8, and 

13 included American wildcelery, water 

stargrass, coontail, Canadian waterweed 

(Elodea canadensis Michx.), and sago 

pondweed (Stukenia pectinatus [L.] Boerner; 
10

Figure 2.1. Presence of submersed aquatic vegetation in a section of Pool 8, Upper Mississippi River, on the basis of 1998 to 2002 data 

pooled together. The map and associated statistics are intended to display the lateral gradient of distribution in relation to water depth 

(April 15– 

from th 

focuses on a small section of the pool to reduce to help clarify the within-pool longitudinal pattern (refer to Figure 2.2).

Main 

channel

Main channel 

border

Side

channel

Contiguous 

backwater

Isolated 

backwater

Number of sites nsa 143 316 532 12

Percent frequency nsa 11.0 (0.5)b 39.5 (0.5) 81.5 (0.5) 89.5 (0.5)

Average velocity (cm/sec) 105 (23) 79 (28) 38 (30) 5 (15) 1 (2)

Average depth (ft) 5.2 (1.1) 2.1 (1.1) 1.6 (1.1) 1.0 (0.7) 0.4 (0.4)

Average distance to nearest land mass (m) 600 (45) 535 (115) 245 (370) 385 (435) 25 (30) a

Submersed aquatic vegetation does not survive in the main channel therefore it was not sampled (ns)

b

Standard deviation
11

Figure 2.2. Presence of submersed aquatic vegetation in Pool 8, Upper Mississippi River, on the basis of 1998–2002 data pooled 

together. 

d 

unp 

mass 

the latter gradient.

Lower Pool 8 Mid Pool 8 Upper Pool 8

Number of sites 1,066 1,405 603

Percent frequency 37.5 (0.5)a 40.5 (0.5) 13.0 (0.5)

Average velocity (cm/sec) 28 (11) 34 (25) 54 (34)

Average depth (m) 1.5 (0.6) 1.5 (0.9) 2.7 (1.4)

Average distance to nearest land mass (m) 2,510 (730) 1220 (960) 250 (170) a

Standard deviation
12

Table 2.1. Percent frequency of occurrence for aquatic vegetation collected during stratified random sampling in upper and 

lo , 

Long Term Resource Monitoring Program from 1998 to 2002 (upper and lower Pool 4 and Pools 5, 7, 11, and 12 do not include 

the isolated backwater stratum). 

1998 1999 2000 2001 2002

Pool Frqa Stdb nc Frq Std n Frq Std n Frq Std n Frq Std n

Submersed vegetation

Upper Pool 4d 21.8 3.0 187 18.5 2.7 213 13.8 2.2 245 7.0 1.6 245 9.7 1.9 245

Lower Pool 4d 49.1 3.0 288 48.9 2.9 302 55.3 2.7 354 57.1 2.7 351 50.9 2.7 355

Pool 5 nse ns ns ns 31.6 2.3 404

Pool 7 ns ns ns ns 57.4 2.5 392

Pool 8 49.3 2.2 516 58.1 2.0 595 47.7 2.0 649 47.5 1.9 670 53.4 2.0 644

Pool 11 ns ns ns 16.3 1.5 564 ns

Pool 12 ns ns ns ns 15.2 1.8 404

Pool 13 43.2 2.2 531 41.9 2.1 550 43.0 2.1 578 41.7 2.0 606 43.0 2.1 579

Pool 26 0.5 0.4 312 0.1 0.1 437 0.2 0.3 262 0.0 0.0 279 0.2 0.3 215

Lower Alton Pool 14.1 2.4 207 1.4 0.8 210 12.4 2.8 135 5.4 2.0 134 5.2 2.1 114

Upper Alton Pool ns ns ns ns 0.0 0.0 408

La Grange Pool 0.0 0.0 463 0.0 0.0 537 0.0 0.0 368 0.0 0.0 357 0.0 0.0 369

Rooted Floating-Leaf Vegetation

Upper Pool 4 1.1 0.8 187 1.6 0.9 213 1.3 0.7 245 0.8 0.6 245 1.6 0.8 245

Lower Pool 4 24.9 2.6 288 17.9 2.2 302 17.1 2.0 354 13.8 1.8 351 17.4 2.0 355

Pool 5 ns ns ns ns 15.1 1.8 404

Pool 7 ns ns ns ns 17.2 1.9 392

Pool 8 18.0 1.7 516 19.0 1.6 595 18.9 1.5 649 18.1 1.5 670 20.7 1.6 644

Pool 11 ns ns ns 7.5 1.0 564 ns

Pool 12 ns ns ns ns 13.5 1.7 404

Pool 13 18.2 1.7 531 20.4 1.7 550 22.0 1.7 578 23.7 1.7 606 25.0 1.8 579

Pool 26 1.2 0.6 312 1.1 0.5 437 2.7 1.0 262 0.8 0.5 279 2.7 1.1 215

Lower Alton Pool 10.9 2.2 207 2.1 1.0 210 6.2 2.1 135 9.8 2.6 134 6.1 2.2 114

Upper Alton Pool ns ns ns ns 0.0 0.0 408

La Grange Pool 0.3 0.3 463 0.5 0.3 537 6.0 1.2 368 0.3 0.3 357 2.2 0.8 369

Emergent Vegetation

Upper Pool 4 2.3 1.1 187 4.7 1.5 213 3.1 1.1 245 3.7 1.2 245 3.5 1.2 245

Lower Pool 4 14.8 2.1 288 10.9 1.8 302 11.4 1.7 354 11.9 1.7 351 12.8 1.8 355

Pool 5 ns ns ns ns 4.1 1.0 404

Pool 7 ns ns ns ns 16.0 1.9 392

Pool 8 11.2 1.4 516 15.0 1.5 595 11.5 1.3 649 9.9 1.2 670 16.4 1.5 644

Pool 11 ns ns ns 564 ns

Pool 12 ns ns ns ns 7.3 1.3 404

Pool 13 3.4 0.8 531 4.7 0.9 550 4.6 0.9 578 5.7 0.9 606 5.0 0.9 579

Pool 26 4.6 1.2 312 7.3 1.3 437 7.4 1.6 262 1.6 0.8 279 10.2 2.1 215

Lower Alton Pool 4.2 1.4 207 0.0 0.0 210 3.5 1.6 135 15.6 3.2 134 13.9 3.3 114

Upper Alton Pool ns ns ns ns 4.6 1.0 408

La Grange Pool 2.6 0.7 463 2.8 0.7 537 1.3 0.6 368 0.9 0.5 357 2.6 0.8 369

a

Percent frequency of occurrence

b

Standard error

c

Number of sites

d

For analysis, Pool 4 was divided into upper (above river mile 775) and lower (below river mile 775) sections

e

Not sampled
13

Appendixes C and D). American wildcelery 

and water stargrass were most prominent in 

the impounded areas where current velocity 

is moderate, whereas coontail, Canadian 

waterweed, and sago pondweed were most 

prominent in isolated and contiguous backwater 

areas with little or no current (Figure 2.4). Sago 

pondweed was consistently recorded in the 

isolated backwaters of lower Alton Pool, whereas 

Eurasian watermilfoil (Myriophyllum spicatum

L.) dominated the floodplain lakes of La Grange 

Pool.

Temporal Dynamics

Because transect data were collected from 

nonrandomly selected backwaters, pool-wide 

estimators from pooling of the backwaters were 

not anticipated to match pool-wide estimators 

from pooling of randomly selected SRS sites. 

The transect sampling data revealed that the 

frequency of occurrence of SAV varied among 

the years as well as between spring and summer 

sampling windows. In upper Pool 4 (Figure 2.5), 

summer estimates were consistently lower than 

the spring estimates. Early senescence of sago 

pondweed, the dominant species in upper Pool 4, 

was a possible cause. The SRS data collected 

between spring and summer transect sampling 

windows followed the trend of the spring 

data in the overlapping years. In lower Pool 4 

(Figure 2.6), spring and summer data showed 

similar trends. The SRS data displayed the same 

pattern as the transect data between 1998 and 

2000. In Pool 8, SRS data also agreed well with 

transect data on the trend of change from 1998 

to 2000 (Figure 2.7). The difference between 

the two trend lines from 2000 to 2001 was likely 

related to a planned water level reduction in 

summer 2001 that dewatered a much greater 

proportion of the transect sampling sites than the 

SRS sites. Pool 13 displayed greater fluctuations 

between spring and summer data, especially in 

1991 and 1993. The distinct differences between 

spring and summer in 1991 and 1993 reflect 

real changes most likely the results of excessive 

water turbidity in summer 1991 and record 

flooding in summer 1993, respectively. However, 

the discrepancy between spring and summer in 

2000 was caused by omission (because of time 

Figure 2.3. Mean total suspended solids in main channel and backwater strata in Long Term Resource Monitoring Program key pools 

during summer stratified sampling from 1993 through 2001. Error bars represent one standard deviation. Courtesy of Rob Burdis, 

Minnesora Department of Natural Resources, Long Term Resource Monitoring Program, Lake City Field Station.
14

Figure 2.4. Presence of selected submersed aquatic species in Pool 13, Upper Mississippi River, from 1998 to 2002.

Figure 2.5. Percent frequency of submersed aquatic species from different sampling efforts by year in upper Pool 4 (above river mile 

775), Upper Mississippi River. Upper Pool 4 was not sampled in spring 2000 because of time constraints.

American wildcelery water stargrass sago pondweed coontail Canadian waterweed

Year

Percent Frequency 
15

Percent Frequency

Year

Figure 2.6. 

Upper Mississippi River. Lower Pool 4 was not sampled in spring 2000 because of time constraints.

Year

Percent Frequency

Figure 2.7. Percent frequency of submersed aquatic species from different sampling efforts by year in Pool 8, Upper Mississippi River.
16

constraints) of two heavily vegetated backwater 

areas during summer sampling (Appendix A). 

Had the omission not occurred, the transect and 

SRS data both would indicate that SAV growth 

in Pool 13 remained steady from 1998 to 2000 

(Figure 2.8). No transects were established in 

Pool 26 because of a lack of sizable aquatic 

vegetation beds (Figure 1.5). Pool-wide SRS 

from 1998 to 2002 confirmed that SAV in Pool 

26 is extremely rare (Figure 2.9). In lower Alton 

Pool, where SAV was found, the transect and 

SRS data clearly showed similar trends from 

1998 to 2000 (Figure 2.9). In La Grange Pool, 

one transect area was established in the main 

stem of the Illinois River (Grape Island, Figure 

1.6) where a small amount of sago pondweed 

was found in 1992, 1993, 1994, and 1999. No 

SAV was found in a poolwide SRS survey from 

1998 to 2002. However, SAV was found in 

floodplain lakes not connected to the Illinois 

River (Figure 2.10). 

 The above analyses established legitimacy 

for merging the transect trend with the SRS 

trend to form a continuous trend from 1991 to 

2002. We found the trends varied between the 

river reaches (Figures 2.5–2.10). In upper Pool 

4, SAV declined steadily from 1991 to 2002. 

The SAV in lower Pool 4 declined steadily from 

1991 to 1996, followed by a moderate recovery 

thereafter. The SAV in Pool 8 experienced a 

major setback in summer 1991 after the spring 

transect sampling and recovered slowly but 

steadily thereafter until 1999 when SAV growth 

peaked and exceeded the spring 1991 level 

(Figure 2.6). As of 2002, SAV in Pool 8 was 

near the peak recorded in 1999. The SAV in Pool 

13 experienced summer setbacks in 1991 and 

in 1993. However, an immediate and complete 

recovery followed each setback. The patterns 

indicate a high degree of resilience to brief 

setbacks and high stability of SAV growth in 

Pool 13 during the period of record. The SRS 

data collected from 1998 to 2002 in Pool 26 and 

La Grange Pool revealed the extreme scarcity of 

SAV growth in the two pools. No transects were 

established in the rivers and their contiguous 

backwaters indicate the same situation was true 

in 1991–1997. The lower Alton Pool supported 

SAV growth in most years since 1991, especially 

during spring time (Figure 2.9).

Figure 2.8. Percent frequency of submersed aquatic species from different sampling efforts by year in Pool 13, Upper Mississippi 

River. Data from spring 2000 was not included in the analysis because two backwaters were not sampled because of time 

constraints.
17

Year

Percent Frequency

Year

Percent Frequency

Figure 2.9. Percent frequency of submersed aquatic species from different sampling efforts by year in Pool 26, Upper Mississippi 

River, and the lower 12 miles of Alton Pool, Illinois River. Transect sites were from backwaters of the Illinois River. Transects were 

not sampled in the summer of 1994 because they were dewatered to promote annual vegetation growth for waterfowl.

Figure 2.10. Percent frequency of submersed aquatic species from different sampling efforts by year in La Grange Pool, Illinois 

River. Transects were in floodplain lakes not influenced by the Illinois River. These areas correspond to the lakes stratum used in 

stratified random sampling. The lake stratum was not included in the pool-wide estimate for La Grange Pool.
18

Chapter 3: Outpool Sampling

The general design of the LTRMP monitoring 

operates under the assumption that the six key 

pools represent a wide spectrum of UMRS 

habitats. We tested the validity of the assumption 

with regard to aquatic vegetation. Field data were 

collected using the SRS protocol in Pool 11 in 

2001 and in Pools 5, 7, 12, and upper Alton Pool 

in 2002. Our approach examined the similarity of 

species composition and of community structure 

between the key pools and the outpools. For 

species composition, we wanted to know how 

many species recorded in the outpools were not 

recorded in the key pools and, conversely, how 

many species recorded in the key pools were 

not recorded in the outpools. If the key pools 

represented a wide spectrum of habitats within 

the UMRS, the number of species unique to the 

out pools would be small. In terms of community 

structure, we wanted to know how similar or 

dissimilar the outpools were to the key pools. 

Methods

We conducted a detrended correspondence 

analysis of the species–sample matrix with 

down-weighting of infrequent species using the 

CANOCO 4.5 software (ter Braak and Smilauer 

2002). The input dataset is a species–sample 

matrix. Each sample represents one pool in 

one year, consisting of the percent frequency 

of occurrence values of individual species 

(columns). All aquatic vegetation species, 

including submersed, emergent, and rooted 

floating-leaf species were included in the matrix. 

All SRS data collected from 1998 to 2002 were 

used in the analysis.

Results

Fifty-six species were found in the five 

outpools, 51 of which were found in the key 

pools. The five species not found in the key pools 

included an unidentified species of horsetail 

(Equisetum spp.), dotted smartweed (Polygonum 

punctatum Elliot), and an unidentified 

watercrowfoot (Ranunculus spp.) found in Pool 

7, and tufted lovegrass (Eragrostis pectinacea

[Michx] Nees x Steud.) and graybark grape (Vitis 

cinerea [Engelm.] Millard) found in upper Alton 

Pool. In comparison, 121 species were recorded 

in the key pools, 70 of which were not found in 

the five outpools. The number of new species 

found in the outpool sampling was small and the 

new species were common components of the 

more xeric terrestrial habitats. 

The first and second ordination axes accounted 

for 34% of the variance of the sample–species 

matrix, which indicated the patterns revealed 

on the two-dimensional ordination plane were 

not particularly strong. This is not surprising 

given our understanding of the biological and 

ecological complexity of the UMRS and that all 

species rather than a selected few were included 

in the analysis. The ordination chart revealed 

that all the outpool samples fell within the space 

formed by the key pools (Figure 3.1). Pools 5 

and 7 were similar to lower Pool 4 and Pool 8 

and they formed a tight cluster. Pools 11 and 12 

fell between Pool 13 and upper Pool 4 and were 

not as tightly clustered. Upper Alton Pool of the 

Illinois River falls into the domain of Pool 26 

of the Mississippi River and La Grange Pool of 

the Illinois River. Upper Pool 4 appeared to be 

out-of-place in the aquatic vegetation species 

ordination plane and the pattern indicates upper 

Pool 4 was more similar to Pool 13 than to lower 

Pool 4 and Pool 8 (Figure 3.2). 
19

Figure 3.1. Detrended correspondence analysis (ordination) of study areas based on frequency of 

occurrence of all aquatic species from 1998 to 2002. For analysis, Pool 4 was divided into upper (above 

river mile 775) and lower (below river mile 775) sections.

Figure 3.2. Correlation between percent frequency of submersed aquatic vegetation and two environmental 

factors, mean water turbidity (calculated from measurements taken between May 1 and August 31 from 

one Long Term Resource Monitoring Program fixed site near the main channel at the upper end of each pool 

or section) and water level fluctuations (standard deviation of daily water levels), by pool (r2 = 0.82). For 

analysis, Pool 4 was divided into upper (above river mile 775) and lower (below river mile 775) sections.

Axis 1

Axis 2
20

Chapter 4: Environmental Factors

Many factors could limit SAV in a river system. 

For the UMRS, small-scale field studies and 

laboratory experiments have confirmed light 

and nutrients as limiting factors (Kimber et al 

1995; Rogers et al. 1995; Korschgen et al. 1997). 

Sediment related factors eradicated SAV from 

the Illinois River during the 1950s (Mills et al. 

1966; Bellrose et al. 1979; Sparks et al. 1990). 

A general belief among the biologists on the 

UMR is that the system-wide pattern of SAV 

is dictated by water turbidity (i.e., the general 

lack of SAV in the lower reaches is because of 

excessively high water turbidity; Rogers and 

Theiling 1998). Whereas this hypothesis was 

supported by anecdotal evidence, it had yet to 

be tested with scientific data. In this chapter we 

explored whether or not high turbidity and water 

level fluctuation were related to the lack of SAV 

(Barko et al. 1986; Rorslett and Johansen 1996; 

Blanch et al. 1998; Bini et al. 1999; Doyle and 

Smart 2001). 

Methods

An analysis of variance was conducted using 

the general linear model procedure of SAS (SAS 

Institute Inc. 1999). The dependant variable 

was the annual frequency of occurrence of SAV 

from 1998 to 2002 computed using the SRS 

data. The explanatory variables were the mean 

water turbidity and the standard deviation of 

daily water levels, May 1–August 31. Mean 

water turbidity was computed using the fixed-site 

monitoring data collected biweekly by the 

LTRMP water quality component (Soballe and 

Fischer 2004). Among the many fixed sites 

monitored by the LTRMP, we selected one site 

in the main channel at the upper end of each 

pool or section so water turbidity measurements 

represented inflow conditions (Table 4.1). 

Water level fluctuation was quantified using the 

standard deviation of the daily water levels at the 

closest gage station operated by the U.S. Army 

Corps of Engineers (Table 4.1). 

Results

Our analysis revealed a negative correlation 

between the two physical factors, water turbidity 

and water level fluctuation, and the percent 

frequency of SAV (Table 4.2; Figure 3.2). 

Together, the two variables accounted for 82% 

of the variance in SAV frequencies (r2 = 0.82). 

Turbidity was a much stronger predictor of SAV 

than water level fluctuation (Type III sum of 

square 4,464 versus 1,392 in Table 4.2).

We examined whether the correlations 

between SAV and turbidity and between SAV 

and water level fluctuation were artifacts of a 

strong longitudinal gradient along the UMRS 

from north to south for all three variables (SAV 

[decreasing], water turbidity [increasing], and 

water level fluctuation [increasing]). If our 

hypothesis was true, turbidity and water level 

fluctuation would become obsolete predictors of 

SAV in the presence of river mile as a predictor 

in the model. A test revealed that our suspicion 

was not warranted. Turbidity and water level 

fluctuation continued to be strong predictors 

despite the presence of river mile. Thus, river 

mile was a nonsignificant predictor in the 

presence of turbidity and water level fluctuation 

in the model (Table 4.3).

Our analyses also revealed that the turbidity 

and water-level fluctuation were good predictors 

of the longitudinal variation but poor predictors 

of yearly variation of SAV. Whereas pools with 

less turbid and less fluctuating water had higher 

frequencies of SAV presence than pools with 

more turbid and more fluctuating pools, years 

of less turbid and less fluctuating water did not 

consistently have higher frequencies of SAV 

presence than years of more turbid and more 

fluctuating water. Additional analyses revealed 

that water depth should be considered together 

with turbidity and water level fluctuation 

to explain the yearly variations. Additional 

publications are planned to describe this 

evaluation in greater detail. 
21

Table 4.1. Long Term Resource Monitoring Program water quality sites and U.S. Army Corps of Engineers gage station by pool.

Pool River Water quality site Gage station

Upper Pool 4 Mississippi M796.9N Lock and Dam 3 tailwater elevation, Welch, Minnesota

Lower Pool 4 Mississippi M764.3A Lock and Dam 4 pool elevation, Alma, Wisconsin

Pool 8 Mississippi M701.1B Lock and Dam 8 pool elevation, Genoa, Wisconsin

Pool 13 Mississippi M556.4A Lock and Dam 13 pool elevation, River Mile 522.4

Pool 26 Mississippi M241.4K Melvin Price Lock and Dam pool elevation, Alton, Illinois

Alton Pool Illinois I007.0W Alton - Grafton

La Grange Pool Illinois I157.8D La Grange Lock and Dam pool elevation, River Mile 80.2

Table 4.2. Results from an analysis of variance to determine the effects of turbidity and water level elevation on the percent 

frequency of submersed aquatic vegetation (r2 = 0.82), Long Term Resource Monitoring Program, Upper Mississippi River 

System.

Source DF Sum of squares Mean square F-value P-value

Model 2 14,205 7,102 75.15 <0.0001

Type I

Water turbidity 1 12,812 12,812 135.57 <0.0001

Water level fluctuation 1 1,392 1,392 14.73 0.0006

Type III

Water turbidity 1 4,464 4,464 47.23 <0.0001

Water level fluctuation 1 1,392 1,392 14.73 0.0006

Error 32 3,024 95

Corrected total 34 17,229

Table 4.3. Results from an analysis of variance to determine the effects of turbidity, water level elevation, and river mile 

on the percent frequency of submersed aquatic vegetation (r2 = 0.84), Long Term Resource Monitoring Program, Upper 

Mississippi River System.

Source DF Sum of Squares Mean Square F-value P-value

Model 3 9,611 3,203 38.90 <0.0001

Type I

River mile 1 3,546 3,546 43.06 <0.0001

Water turbidity 1 5,080 5,080 61.69 <0.0001

Water level fluctuation 1 984 984 11.96 0.0024

Type III

River mile 1 62 62 0.76

Water turbidity 1 2,068 2,068 25.12 <0.0001

Water level fluctuation 1 984 984 11.96 0.0024

Error 21 1,729 82

Corrected total 24 11,341
22

Chapter 5: Habitat Rehabilitation and 

Enhancement Project

Habitat Rehabilitation and Enhancement 

Projects (HREP) and the LTRMP are two key 

elements of the Environmental Management 

Program (U.S. Army Corps of Engineers 1997). 

As an HREP, the U.S. Army Corps of Engineers 

constructed two rock sills and seven sand islands 

topped with silt and clay soils in the impounded 

area of Pool 8 near Stoddard, Wisconsin. The 

construction of the Stoddard HREP started in 

October 1997 and was completed in August 

1998. Approximately 600 acres of aquatic area 

was enclosed and flow velocity and wave action 

were reduced. 

Major goals of the project were to (1) improve 

habitat conditions for backwater fish species 

with an emphasis on habitat for Centrarchids, 

(2) increase high quality waterfowl habitat to 

600 acres and then maintain, and (3) create 

habitat for migratory birds other than waterfowl 

(Neotropical migrants, marsh and water birds, 

and shorebirds). Additional goals include 

increasing turtle nesting habitat; restoring 

habitat for mammals (primarily beaver, mink, 

and muskrats), reptiles, and amphibians; and 

improving conditions for the reestablishment of 

roosting habitat for species such as bald eagles, 

peregrine falcons, and other raptors (USACE 

1996). A matrix of physical and biotic criteria 

were set a priori, including levels of dissolved 

oxygen, current velocity, water depth, cover of 

aquatic vegetation, etc. Although aerial photos 

collected before and after the construction have 

often been used to demonstrate the unmistakable 

success of aquatic vegetation growth, 

species-level information was not included. Our 

objective was to document changes in species 

composition and abundance in the HREP area.

Methods

We delineated the HREP enclosed area and 

an adjacent area to the west and treated them as 

a treatment-control pair (Figure 5.1). Because 

the two areas did not have identical initial 

conditions (in 1997), we were looking for distinct 

differences between them in aquatic vegetation 

changes from 1998 to 2002. An index of 

abundance for individual species and for different 

life forms (submersed, emergent, and rooted 

floating-leaf vegetation) was computed using the 

SRS data. Because of small sampling size in the 

treatment area (14–19 sites yearly), quantification 

of aquatic vegetation was based on the abundance 

index (Yin et al. 2000a), which is more sensitive 

to changes than the frequency of occurrence 

index. The abundance index incorporates 

different formulas depending on the life form of 

the plants. For emergent and rooted floating-leaf 

species, the abundance index corresponds to the 

visually estimated percent cover categories (0%, 

20%, 40%, 60%, 80%, 100%). For SAV, the 

abundance index is computed using the following 

formula (Yin e al. 2000a):

 100

14.6260

3 1

6

1

log 2(1 )

)

6

6

1

( )

log 2(1

 

  













 i

Vi

i

Ri Vi

A

where Vi is the presence/absence (1,0) and Ri is 

the plant density ranking (0,1,2,3,4,5) data for the 

i

th subsampling areas at the site (i=1,2,3,4,5,6). 

Data are treated before computation so that Vi=1 

if Ri >= 1 and, vice versa, Ri >= 1 if Vi=1.

Results

At the time of HREP construction in summer 

1998, the treatment area had a less diverse and 

less abundant aquatic vegetation community 

compared with the control area. The treatment 

area contained 6 submersed species and no 

emergent and rooted floating-leaf species, as 

compared to 11 submersed, 1 emergent, and 

2 rooted floating-leaf species contained in the 

control area (Tables 5.1 and 5.2). In the following 

4 years, eight new species (four submersed, 

two rooted floating-leaf, and two emergent) 

were collected. The abundance index of SAV 

increased from 7.4 to 24.8; and the cover of 

rooted floating-leaf vegetation increased from 

nonexistant to 24.8%; and cover of emergent 

vegetation increased from nonexistant to 5.2% 

(Table 5.2; Figure 5.2). In contrast, the control 

area displayed a general decline in submersed 

and rooted floating-leaf aquatic vegetation and 
23

no statistically significant increase in emergent 

vegetation during the same period. Not all 

species were recorded in every year in the 

control area, but the pattern of hits and misses 

is the result of random chance rather than new 

colonization (Table 5.1). 

As of summer 2002, the fourth growing season 

after completion of construction, coontail, 

Canadian waterweed, and American lotus 

(Nelumbo lutea [Willd.] Pers) maintained a 

strong momentum of growth in the treatment 

area. In contrast, American wildcelery increased 

between 1999 and 2000 and its distribution and 

abundance leveled off thereafter (Figure 5.3). 

The distributional pattern is that SAV dominates 

the water column in deeper (> 0.5 m) regions 

and American lotus dominates the surface of 

shallower (< 0.5 m) regions. Plant responses in 

the Stoddard HREP area are still unfolding and 

much more will be learned in the coming years. 

Knowledge accumulated here can be used in 

HREP design to promote specific vegetation 

assemblages.

Figure 5.1. Treatment and control area in the impounded area near 

Stoddard, Wisconsin, in Pool 8, Upper Mississippi River.
24

Table 5.1. Abundance index by species outside the Stoddard Bay Habitat Rehabilitation and Enhancement Project area of Pool 8, Upper 

Mississippi River System.

Scientific name Common name

1998

(n = 96)

1999

(n = 115)

2000

(n = 132)

2001

(n = 108)

2002

(n = 108)

All submersed species 11.2 ± 1.0 8.1 ± 0.6 3.9 ± 0.4 3.7 ± 0.4 6.6 ± 0.6

Ceratophyllum demersum coontail 1.8 ± 0.4 2.3 ± 0.4 0.9 ± 0.2 0.9 ± 0.2 2.0 ± 0.4

Chara spp. muskgrass 0.0 ± 0.0 0.1 ± 0.1 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Elodea canadensis Canadian waterweed 6.9 ± 0.9 2.9 ± 0.4 0.8 ± 0.2 1.6 ± 0.3 3.9 ± 0.5

Heteranthera dubia water stargrass 3.7 ± 0.5 3.2 ± 0.4 2.6 ± 0.3 2.1 ± 0.3 4.5 ± 0.5

Myriophyllum spicatum Eurasian watermilfoil 1.1 ± 0.2 1.4 ± 0.3 0.3 ± 0.1 0.3 ± 0.1 1.9 ± 0.3

Najas flexilis nodding waternymph 0.1 ± 0.1 1.2 ± 0.4 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Potamogeton crispus curly pondweed 0.6 ± 0.2 0.8 ± 0.2 0.0 ± 0.0 0.7 ± 0.2 0.4 ± 0.2

Potamogeton foliosus/pusillus leafy/small pondweed 0.8 ± 0.2 1.4 ± 0.3 0.0 ± 0.0 0.2 ± 0.1 0.2 ± 0.1

Potamogeton nodosus longleaf pondweed 0.3 ± 0.1 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.2 ± 0.1

Potamogeton zosteriformis flatstem pondweed 0.0 ± 0.0 0.0 ± 0.0 0.2 ± 0.1 0.0 ± 0.0 0.0 ± 0.0

Stuckenia pectinatus sago pondweed 2.4 ± 0.4 1.4 ± 0.2 0.7 ± 0.2 1.3 ± 0.3 1.2 ± 0.3

Vallisneria americana American wildcelery 2.6 ± 0.5 1.5 ± 0.3 1.2 ± 0.3 1.0 ± 0.2 2.0 ± 0.3

Zannichellia palustris horned pondweed 0.4 ± 0.2 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

All rooted floating-leaf species 12.0 ± 2.1 10.1 ± 1.9 3.8 ± 1.1 1.4 ± 0.6 3.4 ± 0.6

Nelumbo lutea American lotus 10.5 ± 1.9 6.2 ± 1.6 3.8 ± 1.1 1.4 ± 0.6 3.1 ± 0.6

Nymphaea odorata white waterlily 1.9 ± 0.8 3.9 ± 1.0 0.0 ± 0.0 0.0 ± 0.0 0.4 ± 0.2

All emergent species 0.4 ± 0.2 5.2 ± 1.4 0.1 ± 0.1 0.0 ± 0.0 1.9 ± 0.6

Eleocharis spp. spikerush 0.0 ± 0.0 0.5 ± 0.2 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Phalaris arundinacea reed canarygrass 0.0 ± 0.0 0.8 ± 0.4 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Sagittaria latifolia broadleaf arrowhead 0.0 ± 0.0 4.6 ± 1.3 0.0 ± 0.0 0.0 ± 0.0 1.5 ± 0.6

Sagittaria rigida stiff arrowhead 0.4 ± 0.2 0.5 ± 0.2 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Schoenoplectus fluviatilis river bulrush 0.0 ± 0.0 0.5 ± 0.2 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Typha latifolia common cattail 0.0 ± 0.0 0.5 ± 0.2 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0

Table 5.2. Abundance Index by species inside the Stoddard Bay Habitat Rehabilitation and Enhancement Project area of Pool 8, Upper 

Mississippi River System.

Scientific name Common name

1998

(n = 27)

1999

(n = 29)

2000

(n = 27)

2001

(n = 35)

2002

(n = 35)

All submersed species 7.4 ± 0.8 17.4 ± 1.5 16.0 ± 0.8 17.7 ± 1.1 24.8 ± 0.8

Ceratophyllum demersum coontail 0.0 ± 0.0 1.6 ± 0.4 5.0 ± 0.7 10.6 ± 0.7 19.5 ± 1.0

Elodea canadensis Canadian waterweed 3.4 ± 0.5 12.5 ± 1.1 13.4 ± 0.8 15.2 ± 1.3 18.8 ± 0.9

Heteranthera dubia water stargrass 4.3 ± 0.6 12.0 ± 1.4 11.3 ± 0.8 10.3 ± 0.9 11.0 ± 0.6

Myriophyllum spicatum Eurasian watermilfoil 0.4 ± 0.2 2.3 ± 0.5 5.1 ± 0.6 6.8 ± 0.8 11.0 ± 0.7

Najas flexilis nodding waternymph 0.0 ± 0.0 0.0 ± 0.0 1.6 ± 0.4 1.0 ± 0.4 0.0 ± 0.0

Potamogeton crispus curly pondweed 0.0 ± 0.0 1.5 ± 0.3 1.3 ± 0.4 3.5 ± 0.6 0.9 ± 0.2

Potamogeton foliosus/pusillus leafy/small pondweed 0.0 ± 0.0 0.0 ± 0.0 2.9 ± 0.4 2.9 ± 0.5 2.6 ± 0.5

Potamogeton nodosus longleaf pondweed 0.7 ± 0.3 0.0 ± 0.0 0.4 ± 0.1 1.2 ± 0.4 0.9 ± 0.4

Potamogeton richardsonii Richardson’s pondweed 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.9 ± 0.2

Potamogeton zosteriformis flatstem pondweed 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.4 ± 0.2

Stukenia pectinatus sago pondweed 2.7 ± 0.6 1.8 ± 0.6 2.2 ± 0.5 2.6 ± 0.6 1.9 ± 0.4

Vallisneria americana American wildcelery 2.2 ± 0.4 1.3 ± 0.5 8.9 ± 0.7 10.3 ± 0.8 10.5 ± 0.8

All rooted floating-leaf species 0.0 ± 0.0 0.0 ± 0.0 2.2 ± 0.6 7.6 ± 1.0 24.8 ± 2.9

Nelumbo lutea American lotus 0.0 ± 0.0 0.0 ± 0.0 2.2 ± 0.6 5.0 ± 0.9 18.3 ± 2.6

Nymphaea odorata white waterlily 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 3.9 ± 0.8 5.2 ± 2.1

All emergent species 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 5.2 ± 1.6

Sagittaria latifolia broadleaf arrowhead 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 3.9 ± 1.6

Sagittaria rigida stiff arrowhead 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 2.6 ± 0.7
25

Figure 5.2. Abundance index for submersed, rooted floating-leaf, 

and emergent aquatic vegetation in the Stoddard Bay Habitat 

Rehabilitation and Enhancement Project (HREP) and control area, 

Upper Mississippi River.

Figure 5.3. Abundance index of American wildcelery (Vallisneria 

americana Michx.), coontail (Ceratophyllum demersum L.), and 

Canadian waterweed (Elodea canadensis Michx.) and percent 

cover of American lotus (Nelumbo luteo Willd.) in the Stoddard 

Bay Habitat Rehabilitation and Enhancement Project (HREP) area, 

control area, and Pool 8, Upper Mississippi River.
26

Chapter 6: Summary

Based on our analyses presented in Chapters 

2–5, we conclude:

• Submersed aquatic vegetation beds in the 

Upper Mississippi River System were present 

in higher frequency in areas less influenced by 

flows from the main channels. Deeper water, 

faster velocities, and increased suspended solids 

are related to the distribution and abundance of 

SAV in the UMRS. 

• Within a navigation pool, the mid- and lower 

sections are better habitat than the tailwater 

section for SAV. Slower velocities and shallower 

water may be two factors contributing to this 

difference.

• The dynamics of submersed aquatic 

vegetation from 1991 to 2002 varied among the 

river reaches monitored by the LTRMP. Our data 

revealed that SAV declined steadily from 1991 

to 2002 in upper Pool 4 and only a small fraction 

of SAV beds remained there through 2002. The 

SAV in lower Pool 4 experienced a decline from 

1991 to 1996, followed by a moderate recovery 

still evident in 2002. 

• The LTRMP data in Pool 8 documented a 

major setback in summer 1991 in the aftermath 

of the 1987–89 basin-wide drought as well as a 

process of recovery lasting throughout the 1990s. 

• The SAV growth in Pool 13 displayed a 

high degree of stability over the period of record 

and high degree of resilience against occasional 

summer declines. 

• Presence of SAV in Pool 26 and La Grange 

Pool was extremely rare. 

• Few SAV beds were present in the 

backwaters of the Illinois River within the lower 

12 miles of the Alton Pool.

• Five species out of 56 recorded in the 

five outpools were not among the 121 species 

recorded in the key pools. 

• A detrended correspondence analysis 

indicated the outpools were within the range 

of variation among the key pools. None of the 

outpools we sampled in 2002 were found to be 

drastically different from all the key pools, which 

suggests the LTRMP key pools represent a wide 

spectrum of UMRS habitats. 

• The longitudinal pattern of SAV distribution 

in the UMRS is strongly correlated with water 

turbidity and water level fluctuation (r2=.82). 

Pools with clearer water and less fluctuating 

water levels supported better vegetation growth. 

Turbidity was a stronger predictor of SAV 

abundance than water level fluctuation. 

• The environmental engineering project 

completed in 1998 at Stoddard Bay in Pool 8 

of the Upper Mississippi River has effectively 

promoted plant recolonization. After four 

growing seasons, Ceratophyllum demersum 

L. and Elodea canadensis Michx. dominated 

the water column in deeper (>0.5 m) regions 

and Nelumbo lutea Willd. dominated the 

water surface in shallower (<0.5 m) regions. 

Ceratophyllum demersum and N. lutea continued 

expanding their distribution through 2002.
27

Acknowledgments

We thank Megan Moore of the Minnesota 

Department of Natural Resources, Theresa 

Blackburn of the Iowa Department of Natural 

Resources, Rob Cosgriff and Thad Cook of the 

Illinois Department of Natural Resources who 

led data collection within their assigned areas; 

Brian Ickes and Jim Rogala of USGS who 

provided technical assistance; Jeff Janvrin of 

Wisconsin Department of Natural Resources who 

provided historical information on the Stoddard 

Bay HREP in Pool 8; Dr. Patricia Heglund, Dr. 

Brian Gray, Georgina Ardinger, and several 

anonymous reviewers who provided valuable 

comments. Funding was provided by the U.S. 

Army Corps of Engineers through the Long Term 

Resource Monitoring Program administered by 

the U.S. Geological Survey.

References

Barko, J. W., M. S. Adams, and N. L. Clesceri. 

1986. Environmental factors and their 

consideration in the management of submersed 

aquatic vegetation: a review. Journal of 

Aquatic Plant Management 24:1–10.

Bellrose, F. C., F. L. Paveglio, and D. W. 

Steffeck. 1979. Waterfowl populations and 

the changing environment of the Illinois River 

valley. Illinois Natural History Survey Bulletin, 

Volume 32, Article 1, Urbana. 54 pp.

Belt, C. B. Jr. 1975. The 1973 flood and man’s 

constriction of the Mississippi River. Science 

189:681–684.

Bini, L. M., S. M. Thomaz, K. J. Murphy, and 

A. F. M. Camargo. 1999. Aquatic macrophyte 

distribution in relation to water and sediment 

conditions in the Itaipu Reservoir, Brazil. 

Hydrobiologica 415:147–154.

Blanch, S. J., G. G. Ganf, and K. F. Walker. 

1998. Growth and recruitment in Vallisneria 

americana as related to average irradiance in 

the water column. Aquatic Botany 61:181–205.

Chambers, P. A., E. E. Prepas, H. R. Hamilton, 

and M. L. Bothwell. 1991. Current velocity 

and its effect on aquatic macrophytes in 

flowing waters. Ecological Applications 

1(3):249–257.

Cochran, W. G. 1977. Sampling techniques, 

third edition. John Wiley & Sons, New York. 

428 pp.

Doyle, R. D., and R. M. Smart. 2001. Impacts 

of water column turbidity on the survival and 

growth of Vallisneria americana winterbuds 

and seedlings. Journal of Lake and Reservoir 

Management 17:17–28.

Fischer J. R. , and T. O. Claflin. 1995. Decline 

in aquatic vegetation in Navigation Pool No. 

8, Upper Mississippi River between 1975 

and 1991. Regulated Rivers: Research & 

Management 11:157–165.

Green, W. E. 1960. Ecological changes on the 

Upper Mississippi River Wildlife and Fish 

Refuge since inception of the 9-foot channel. 

U.S. Department of the Interior, Fish and 

Wildlife Service Annual Refuge Report, 

Winona, Minnesota. 17 pp.

Green, W. E. 1984. The great river refuge. 

Pages 431–439 in A. S. Hawkins, R. C. 

Hanson, H. K. Nelson, and H. M. Reeves, 

editors. Flyways: pioneering waterfowl 

management in North America. Supplement of 

documents, U.S. Government Printing Office, 

Washington, D.C., May 1984.

Grubaugh, J. W., and R. V. Anderson. 1989. 

Long-term effects of navigation dams on 

a segment of the Upper Mississippi River. 

Regulated Rivers Research & Management 

4:97–104.

Gutreuter, S. 1997. Fish monitoring by the Long 

Term Resource Monitoring Program on the 

Upper Mississippi River System: 1990–1994. 

U.S. Geological Survey, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, November 1997. LTRMP 97-T004. 

78 pp. + Appendix.

Jessen, R., and R. Lound. 1962. An evaluation 

of survey techniques for submerged aquatic 

plants. Minnesota Department of Conservation, 

Game Investigational Report 6, St. Paul. 10 pp. 
28

Kimber A., J. L. Owens, and W. G. Crumpton. 

1995. Light availability and growth of 

wildcelery (Vallisneria Americana) in Upper 

Mississippi River backwaters. Regulated 

Rivers: Research & Management 11:221–226.

Korschgen, C. E., L. S. George, and W. L. 

Green. 1988. Feeding ecology of canvasbacks 

staging on Pool 7 of the Upper Mississippi 

River. Pages 237–250 in M. W. Weller, editor. 

Waterfowl in winter. University of Minnesota 

Press. Minneapolis.

Korschgen, C. E., and W. L. Green. 1988. 

American wild celery (Vallisneria americana): 

Ecological considerations for restorarion. U.S. 

Fish and Wildlife Service Technical Report 19. 

22 pp.

Korschgen, C. E., W. L. Green, and K. P. 

Kenow. 1997. Effects of irradiance on growth 

and winter bud production by Vallisneria 

americana and consequences to its abundance 

and distribution. Aquatic Botany 58: 1–9. 

Langrehr, H. A. 1992. Summary of vegetation 

sampling for selected transects in Pool 8, 

Upper Mississippi River System, 1990. Annual 

report by the Wisconsin Department of Natural 

Resources, Onalaska, Wisconsin, for the U.S. 

Fish and Wildlife Service, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, October 1992. EMTC 92-S001. 

29 pp. (NTIS # PB94-103728).

Mills, B. H., W. C. Startt, and F. C. Bellrose. 

1966. Man’s effect on the fish and wildlife 

of the Illinois River. Illinois Natural History 

Survey Biological Note 57, Urbana. 24 pp.

Peitzmeier-Romano, S., K. D. Blodgett, and 

R. E. Sparks. 1992. Summary of vegetation 

sampling for selected transects of La Grange 

Pool, Illinois River, 1990. Report by the 

Illinois Natural History Survey, Havana, 

Illinois, for the U.S. Fish and Wildlife Service, 

Environmental Management Technical Center, 

Onalaska, Wisconsin, November 1992. EMTC 

92-S007. 34 pp. (NTIS # PB94-109477).

Rogers, S. J. 1994. Preliminary evaluation 

of submersed macrophyte changes in the 

Upper Mississippi River. Lake and Reservoir 

Management 10:35–38.

Rogers, S., T. Blackburn, D. Dieterman, 

H. Langrehr, J. Nelson, and S. 

Romano-Peitzmeier. 1998. 1991 annual status 

report: A summary of aquatic vegetation 

monitoring at selected locations in Pools 4, 8, 

13, and 26 and La Grange Pool of the Upper 

Mississippi River System. U.S. Geological 

Survey, Environmental Management Technical 

Center, Onalaska, Wisconsin, June 1998, 

LTRMP 98-P005, 21 pp. + Appendixes A–B 

(NTIS #PD98-164510).

Rogers, S. J., D. G. McFarland, and J. W. Barko. 

1995. Evaluation of the growth of Vallisneria 

americana Michx. in relation to sediment 

nutrient availability. Lake and Reservoir 

Management 11(1):57–66.

Rogers, S. J., and T. W. Owens. 1995. Long Term 

Resource Monitoring Program procedures: 

Vegetation monitoring. National Biological 

Service, Environmental Management Technical 

Center, Onalaska, Wisconsin, July 1995. 

LTRMP 95-P002-3. 10 pp. + Appendixes A–E

Rogers, S. J., and C. Theiling. 1998. Submersed 

aquatic vegetation. Pages 8.1–8.11, in K. 

Lubinski and C. Theiling, editors. Ecological 

status and trends of the Upper Mississippi 

River System 1998. U.S. Geological Survey, 

Environmental Management Technical Center, 

Onalaska, Wisconsin, April 1999. LTRMP 

99-T001. 

Rorslett, B., and S. W. Johansen. 1996. Remedial 

measures connected with aquatic macrophytes 

in Norwegian regulated rivers and reservoirs. 

Regulated Rivers: Research & Management 

12:509–522.

SAS Institute Inc. 1999. SAS OnlineDoc. Version 

8. SAS Institute Inc., Cary, North Carolina.

Scarpino, P. V. 1985. Great River: an 

environmental history of the Upper 

Mississippi, 1890–1950. University of 

Missouri Press, Columbia. 219 pp.

Shay, T. A., and R. D. Gent. 1992. Summary of 

vegetation sampling for selected transects in 
29

Pool 13, 1990. Report by the Iowa Department 

of Natural Resources, Bellevue, Iowa, for the 

U.S. Fish and Wildlife Service, Environmental 

Management Technical Center, Onalaska, 

Wisconsin, November 1992. EMTC 92-S015. 

26 pp. (NTIS # PB94-109261).

Simons, D. B., P. F. Lagasse, Y. H. Chen, and S. 

A. Schumm. 1975. The river environment: a 

reference document., U.S. Fish and Wildlife 

Service, Twin Cities, Minnesota. 535 pp.

Soballe, D. M., and J. Fischer. 2004. Long Term 

Resource Monitoring Program Procedures: 

Water quality monitoring. U.S. Geological 

Survey, Upper Midwest Environmental 

Sciences Center, La Crosse, Wisconsin, 2004. 

LTRMP 2003-T001-1 (Ref. 95-P002-5). 72 pp. 

+ Appendixes A–J.

Sparks, R. E. 1984. The role of contaminants 

in the decline of the Illinois River: 

Implications for the Mississippi: Pages 

25–66 in J. G. Wiener, R. V. Anderson, and 

D. R. McConville, editors. Contaminants in 

the Upper Mississippi River. Butterworth 

Publishers, Stoneham, Massachusetts. 

Sparks, R. E., P. B. Bayley, S. L. Kohler, and L. 

L. Osborne. 1990. Disturbance and recovery 

of large floodplain rivers. Environmental 

Management 14:699–709.

ter Braak, C. J. F., and P. Smilauer. 2002. 

CANOCO reference manual and CanoDraw 

for Windows user’s guide: software for 

Canonical Community Ordination (Version 

4.5). Microcomputer Power. Ithaca, New York. 

500 pp.

U.S. Army Corps of Engineers. 1996. Upper 

Mississippi River System Environmental 

Management Program-Pool 8 Island Phase 

II–Habitat Rehabilitation and Enhancement 

Project. Corps of Engineers, St. Paul, 

Minnesota.

U.S. Fish and Wildlife Service. 1993. Operating 

Plan for the Upper Mississippi River System 

Long Term Resource Monitoring Program. 

Environmental Management Technical 

Center, Onalaska, Wisconsin, Revised 

September 1993. EMTC 91-P002R. 179 pp. 

(NTIS # PB94-160199)

U.S. Army Corps of Engineers. 1997. Report 

to Congress: An Evaluation of the Upper 

Mississippi River Environmental Management 

Program. Corps of Engineers, Rock Island, 

Iowa

Vis, C., C. Hudon, and R. Carignan. 2003. An 

evaluation of approaches used to determine 

the distribution and biomass of emergent and 

submersed aquatic macrophytes over large 

spatial scales. Aquatic Botany 77:187–201.

Yeager, L. E. 1949. Effect of permanent flooding 

in a river-bottom timber area. Illinois Natural 

History Survey Bulletin, Urbana, Illinois. 25: 

33–65.

Yin, Y., H. Langrehr, J. Nelson, T. Blackburn, T. 

Cook, and J. Winkelman. 2000a. 1997 annual 

status report: Status and trend of submersed 

and floating-leaf aquatic vegetation in 

thirty-two backwaters in Pools 4, 8, 13, and 26 

and La Grange Pool of the Upper Mississippi 

River System. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin, June, 2000. LTRMP 

2000-P002. 19 pp. + Appendixes A–B (NTIS 

#PB2000-107875).

Yin, Y., J. S. Winkelman, and H. A. Langrehr. 

2000b. Long Term Resource Monitoring 

Program procedures: Aquatic vegetation 

monitoring. U.S. Geological Survey, Upper 

Midwest Environmental Sciences Center, 

La Crosse, Wisconsin, April 2000. LTRMP 

95-O002-7. 8pp. + Appendixes A–C.
A-1

Appendix A. Total number of points sampled along transects by pool and year, 1991–2002

Table A-1. Upper Pool 4 (above Lake Pepin).

Big Lake

Rice Lake/Big 

Lake Bay Catherine Pass

Dead Slough 

Lake

Year Spa Sub Sp Su Sp Su Sp Su

1991 181 177 49 72 77 74 98 93

1992 133 123 58 55 76 76 130 129

1993 152 159 64 56 78 70 133 115

1994 156 149 81 53 78 62 140 136

1995 171 158 90 77 85 80 162 135

1996 182 160 85 80 80 85 136 136

1997 167 148 91 78 88 88 142 143

1998 157 153 71 67 71 74 134 133

1999 165 159 79 79 80 80 136 136

2000 nsc 167 ns 79 80 ns 133 ns

a

Spring

b

Summer

c

Not sampled

Table A-2. Lower Pool 4 (below Lake Pepin).

Goose Lake Mud Lake

Lower Peterson 

Lake

Upper Peterson 

Lake Robinson Lake

Year Sp Su Sp Su Sp Su Sp Su Sp Su

1991 25 25 63 58 94 119 70 61 199 179

1992 26 23 55 56 109 156 71 51 198 168

1993 28 24 57 51 118 132 56 58 187 211

1994 26 27 59 53 115 132 69 72 223 221

1995 31 28 61 68 130 128 77 72 233 227

1996 30 28 63 55 104 128 55 53 228 225

1997 30 28 57 55 127 118 80 80 220 205

1998 25 24 57 54 130 112 69 75 204 213

1999 26 27 55 55 122 122 69 59 210 198

2000 27 ns 55 ns ns 122 ns 71 ns 203
A-2

Table A-3. Pool 8.

Blue Lake

Boomerang 

Island Goose Island

Horseshoe 

Island Lawrence Lake Shady Maple Stoddard 

Year Sp Su Sp Su Sp Su Sp Su Sp Su Sp Su Sp S1991 ns ns ns ns ns 80 ns 40 258 195 24 30 ns n1992 ns ns ns ns 111 113 75 83 261 398 106 105 ns 41993 ns 122 ns 75 114 114 75 82 247 435 114 101 48 41994 112 110 107 102 112 112 76 78 392 407 100 105 47 41995 124 118 104 104 118 113 82 80 422 386 102 104 48 41996 126 118 104 104 112 114 85 82 421 417 102 90 50 41997 126 116 104 104 119 114 90 85 426 402 107 102 50 51998 134 132 104 104 111 115 83 81 434 441 102 106 50 51999 135 123 104 104 117 109 82 90 418 374 105 101 49 52000 ns 135 ns 104 ns 111 ns 88 ns 405 ns 101 ns 52001 ns ns ns 104 ns 78 ns 84 ns 318 ns 100 ns n

Table A-4. Pool 13.

Brown’s Lake Johnson Creek

Johnson Creek 

Levee Pomme de Terre Potter’s Marsh Savannah Bay Spring L

Year Sp Su Sp Su Sp Su Sp Su Sp Su Sp Su Sp 1991 194 235 ns 30 55 40 52 59 49 41 ns 120 ns 1992 280 354 40 56 81 73 69 81 71 41 146 148 126 1993 325 308 53 59 88 82 78 77 77 75 135 150 149 1994 379 390 41 59 83 89 74 82 77 101 151 134 136 1995 367 458 60 70 116 107 75 71 87 94 137 138 176 1996 338 357 59 65 113 102 75 75 96 92 142 139 162 1997 384 421 61 65 123 122 71 81 101 129 143 141 174 1998 431 424 66 67 108 114 68 85 110 132 144 143 153 1999 450 451 72 67 126 124 87 88 126 126 151 151 190 2000 164 455 67 68 ns 124 87 86 ns 126 151 151 189 
A-3

Table A-5. Alton Pool.

Calhoun Point Fuller Lake Stump Lake Swan Lake

Year Sp Su Sp Su Sp Su Sp Su

1991 276 137 ns ns 196 ns 308 80

1992 157 157 32 ns 168 ns 291 282

1993 157 156 29 32 174 194 291 146

1994 155 ns 50 ns 169 ns 276 ns

1995 82 86 29 29 166 155 161 159

1996 156 27 29 37 126 102 ns ns

1997 157 77 29 ns 175 ns 133 133

1998 159 157 29 29 170 174 282 292

1999 157 150 29 41 168 175 292 292

2000 155 ns 34 ns 171 ns 291 ns

Table A-6. La Grange Pool.

Banner Marsh Grape Island Point Lake Spring Lake

Year Sp Su Sp Su Sp Su Sp Su

1991 13 13 ns ns 20 20 105 99

1992 16 16 13 9 20 21 87 86

1993 18 16 21 ns 28 26 144 143

1994 26 22 18 21 25 26 147 146

1995 24 24 21 15 25 26 ns 146

1996 16 17 ns 12 22 22 51 78

1997 14 12 16 16 24 25 119 99

1998 18 18 16 18 25 23 90 92

1999 20 20 16 16 25 25 98 90

2000 18 17 18 18 25 22 100 90
B-1

Appendix B. Percent frequency of occurrence of submersed aquatic vegetation by year, sampling strata, and poo

sampling 1998–2002, Long Term Resource Monitoring Program, Upper Mississippi River Syste

1998 1999 2000 2001 

Stratum Frqa Stdb nc Frq Std n Frq Std n Frq Std n Pool 4 – Isolated Backwater 84.4 6.5 32 81.3 7.0 32 81.3 7.0 32 76.0 6.1 50 Upper Pool 4d – Main Channel Border 0.0 0.0 9 16.7 11.2 12 3.3 3.3 30 3.3 3.3 30 Upper Pool 4 – Secondary Channel 4.3 3.0 47 0.0 0.0 61 0.0 0.0 40 0.0 0.0 40 Upper Pool 4 – Contiguous Backwater 32.4 5.5 74 29.3 5.3 75 18.0 3.9 100 14.0 3.5 100 Upper Pool 4 – Lake Pepin 21.1 5.4 57 16.9 4.7 65 14.7 4.1 75 5.3 2.6 75 Lower Pool 4d – Main Channel Border 10.8 5.2 37 20.8 5.9 48 22.5 6.7 40 22.5 6.7 40 Lower Pool 4 – Secondary Channel 35.4 6.0 65 37.3 6.3 59 45.0 6.5 60 31.7 6.1 60 Lower Pool 4 – Contiguous Backwater 68.8 3.7 157 66.3 3.8 160 64.2 3.6 179 71.0 3.4 176 Lower Pool 4 – Lake Pepin 6.9 4.8 29 8.6 4.8 35 46.7 5.8 75 41.3 5.7 75 Pool 8 – Main Channel Border 18.9 5.4 53 25.7 5.3 70 30.3 4.6 99 24.0 4.3 100 Pool 8 – Secondary Channel 35.5 5.0 93 36.0 4.8 100 32.5 4.3 120 22.5 3.8 120 Pool 8 – Impounded 33.5 3.6 170 44.9 3.3 225 34.7 3.2 225 36.9 3.2 225 Pool 8 – Contiguous Backwater 82.0 2.9 172 92.4 2.0 172 74.9 3.3 175 76.0 3.2 175 Pool 8 – Isolated Backwater 96.4 3.6 28 92.9 5.0 28 93.3 4.6 30 92.0 3.9 50 Pool 13 – Main Channel Border 8.1 3.5 62 11.4 3.8 70 14.3 4.2 70 10.0 3.6 70 Pool 13 – Secondary Channel 14.5 4.5 62 10.0 3.6 70 4.3 2.4 70 14.3 4.2 70 Pool 13 – Impounded 42.6 3.4 209 42.4 3.4 210 40.5 3.4 210 38.3 3.4 209 Pool 13 – Contiguous Backwater 52.4 3.8 170 51.8 3.8 170 58.1 3.5 198 55.6 3.5 198 Pool 13 – Isolated Backwater 71.4 8.7 28 56.7 9.2 30 53.3 9.3 30 57.6 6.5 59 Pool 26 – Main Channel Border 0.0 0.0 121 0.0 0.0 137 0.0 0.0 50 0.0 0.0 49 Pool 26 – Secondary Channel 0.0 0.0 84 0.0 0.0 90 0.0 0.0 50 0.0 0.0 50 Pool 26 – Impounded 0.0 0.0 27 1.3 1.3 80 0.0 0.0 40 0.0 0.0 40 Pool 26 – Contiguous Backwater 2.0 2.0 50 0.0 0.0 80 0.0 0.0 80 0.0 0.0 80 Pool 26 – Isolated Backwater 3.3 3.3 30 0.0 0.0 50 2.4 2.4 42 0.0 0.0 60 Lower Alton Pool – Main Channel Border 0.0 0.0 47 2.0 2.0 50 0.0 0.0 40 0.0 0.0 40 Lower Alton Pool – Isolated Backwater 16.9 3.0 160 1.3 0.9 160 14.7 3.7 95 6.4 2.5 94 La Grange Pool – Main Channel Border 0.0 0.0 83 0.0 0.0 120 0.0 0.0 80 0.0 0.0 78 La Grange Pool – Secondary Channel 0.0 0.0 29 0.0 0.0 40 0.0 0.0 50 0.0 0.0 50 La Grange Pool – Contiguous Backwater 0.0 0.0 172 0.0 0.0 190 0.0 0.0 100 0.0 0.0 100 La Grange Pool – Isolated Backwater 0.0 0.0 179 0.0 0.0 187 0.0 0.0 138 0.0 0.0 129 La Grange Pool – Floodplain Lake nse ns ns ns ns ns 80.7 5.3 57 77.2 5.6 57 

aPercent frequency of occurrencebStandard errorcNumber of sitesdFor analysis, Pool 4 was divided into upper (above river mile 775) and lower (below river mile 775) sectionseNot sampled
C-1

Appendix C. Percent frequency of occurrence by species for Pools 4, 5, and 7 based on 2002 

stratified random sampling, Long Term Resource Monitoring Program, Upper Mississippi 

River System. 

Upper 

Pool 4a

Lower 

Pool 4a Pool 5 Pool 7

n = 245 n = 355 n = 404 n = 392

Common name Scientific name Frqb Stdc Frq Std Frq Std Frq Std

Submersed vegetation

bladderwort, common Utricularia macrorhiza Le Conte 0.0 0.0 0.0 0.0 0.0 0.0 0.6 0.4

buttercup Ranunculus spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.4 0.3

chara Chara spp. 0.0 0.0 0.3 0.3 0.2 0.2 3.2 0.9

coontail Ceratophyllum demersum L. 1.9 0.9 24.4 2.3 12.0 1.6 32.4 2.4

pondweed, curly Potamogeton crispus L. 0.0 0.0 10.5 1.6 3.7 0.9 3.2 0.9

pondweed, flatstem P. zosteriformis Fern. 0.0 0.0 7.3 1.4 2.7 0.8 19.0 2.0

pondweed, horned Zannichellia palustris L. 0.0 0.0 0.3 0.3 0.4 0.3 0.0 0.0

pondweed, leafy/small P. foliosus Raf./P. L. 0.5 0.5 13.0 1.8 5.7 1.2 11.6 1.6

pondweed, longleaf P. nodosus Poir. 0.3 0.3 3.7 1.0 2.8 0.8 2.5 0.8

pondweed, Richardson’s P. richardsonii (Benn.) Rydb. 0.0 0.0 0.0 0.0 0.2 0.2 8.5 1.4

pondweed, sago Stuckenia pectinatus (L.) Boerner 9.1 1.8 8.6 1.5 10.3 1.5 6.4 1.2

stargrass, water Heteranthera dubia (Jacq.) Mac. 0.0 0.0 24.0 2.3 9.8 1.5 24.9 2.2

watermilfoil, Eurasian Myriophyllum spicatum L. 0.0 0.0 19.2 2.1 10.5 1.5 21.0 2.1

watermilfoil, northern M. sibiricum Komarov 0.0 0.0 0.3 0.3 0.0 0.0 0.0 0.0

waternymph, nodding Najas flexilis (Willd.) Rostk. and 

Schmidt 0.3 0.3 4.2 1.1 0.4 0.3 5.4 1.1

waterweed, Canadian Elodea canadensis Michx. 0.5 0.5 21.6 2.2 11.4 1.6 31.6 2.4

wildcelery Vallisneria americana Michx. 0.0 0.0 28.6 2.4 9.1 1.4 43.5 2.5

Rooted floating-leaf vegetation

lotus, American Nelumbo lutea Willd. 0.0 0.0 3.1 0.9 4.6 1.0 8.0 1.4

pond-lily, yellow Nuphar variegata Dur. 0.0 0.0 0.3 0.3 0.4 0.3 0.1 0.2

waterlily, white Nymphaea odorata Ait. 1.3 0.7 12.5 1.8 10.0 1.5 9.2 1.5

Emergent vegetation

arrowhead, broadleaf Sagittaria latifolia Willd. 1.1 0.7 5.8 1.2 0.4 0.3 3.6 0.9

arrowhead, stiff Sagittaria rigida Pursh 0.0 0.0 7.3 1.4 0.0 0.0 8.8 1.4

bulrush, river Schoenoplectus fluviatilis (Torr) 

MT Strong 2.4 1.0 1.2 0.6 0.0 0.0 0.4 0.3

bulrush, softstem Schoenoplectus tabernaemontani

(K.C. Gelm) Palla 0.8 0.6 0.7 0.5 0.6 0.4 0.3 0.3

burreed, giant Sparganium eurycarpum Engelm 

x Gray 0.0 0.0 2.6 0.8 1.8 0.7 1.8 0.7

canarygrass, reed Phalaris arundinacea L. 0.3 0.3 1.3 0.6 1.2 0.6 0.3 0.3

cattail, broadleaf Typha latifolia L. 0.0 0.0 0.0 0.0 0.2 0.2 0.1 0.2

cattail, narrowleaf Typha angustifolia L. 0.3 0.3 0.0 0.0 0.2 0.2 0.1 0.2

cutgrass, rice Leersia oryzoides (L.) Sw. 0.3 0.3 1.0 0.5 0.2 0.2 0.4 0.3

horsetail Equisetum spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2

loosestrife, purple Lythrum salicaria L. 0.0 0.0 0.5 0.4 0.0 0.0 0.0 0.0

pickerelweed Pontederia cordata L. 0.0 0.0 0.9 0.5 0.2 0.2 2.6 0.8

rice, wild Zizania aquatica L. 0.0 0.0 1.2 0.6 0.0 0.0 6.6 1.3

smartweed, dotted Polygonum punctatum Ell. 0.0 0.0 0.0 0.0 0.0 0.0 0.4 0.3

smartweed, water Polygonum amphibium L. 0.0 0.0 0.2 0.3 0.0 0.0 0.7 0.4

spikerush Eleocharis spp. 0.0 0.0 0.6 0.4 0.0 0.0 0.2 0.3

willow, sandbar Salix exigua Nutt. 0.8 0.6 0.0 0.0 0.0 0.0 0.0 0.0 a

For analysis, Pool 4 was divided into upper (above river mile 775) and lower (below river mile 775) sections

b

Percent frequency of occurrence

c

Standard error
D-1

Appendix D. Percent frequency of occurrence by species for Pool 11 in 2001 

and Pools 8, 12, and 13 based on 2002 stratified random sampling, 

Long Term Resource Monitoring Program, Upper Mississippi River System. 

Pool 8 Pool 11 Pool 12 Pool 13

n = 644 n = 568 n = 404 n = 579

Common name Scientific name Frqa Stdb Frq Std Frq Std Frq Std

Submersed vegetation

bladderwort, common Utricularia macrorhiza Le Conte 1.0 0.4 0.0 0.0 0.0 0.0 0.0 0.0

chara Chara spp. 0.5 0.3 0.3 0.2 0.0 0.0 0.6 0.3

coontail Ceratophyllum demersum L. 28.0 1.8 9.1 1.2 9.2 1.4 24.5 1.8

pondweed, curly Potamogeton crispus L. 10.6 1.2 0.8 0.4 0.6 0.4 9.1 1.2

pondweed, flatstem P. zosteriformis Fern. 7.7 1.1 0.7 0.3 0.0 0.0 0.5 0.3

pondweed, horned Zannichellia palustris L. 0.1 0.1 0.0 0.0 0.0 0.0 0.7 0.3

pondweed, leafy/small P. foliosus Raf./P. L. 12.1 1.3 1.1 0.4 0.8 0.4 8.7 1.2

pondweed, longleaf P. nodosus Poir. 3.8 0.8 0.8 0.4 3.9 1.0 4.4 0.9

pondweed, Richardson’s P. richardsonii (Benn.) Rydb. 0.4 0.3 0.0 0.0 0.0 0.0 0.0 0.0

pondweed, sago Stuckenia pectinatus (L.) Boerner 14.5 1.4 9.2 1.2 6.7 1.2 22.8 1.8

stargrass, water Heteranthera dubia (Jacq.) MacM. 28.3 1.8 0.7 0.3 4.4 1.0 9.5 1.2

watermilfoil, Eurasian Myriophyllum spicatum L. 16.9 1.5 2.3 0.6 2.8 0.8 14.1 1.5

waternymph, brittle Najas minor All. 0.0 0.0 0.0 0.0 0.2 0.2 6.3 1.0

waternymph, nodding N. flexilis (Willd.) Rostk. & 

Schmidt 1.6 0.5 0.3 0.2 0.0 0.0 0.0 0.0

waternymph, southern N. guadalupensis (Spreng.) 

Magnus 0.0 0.0 1.4 0.5 0.0 0.0 2.1 0.6

waterweed, Canadian Elodea canadensis Michx. 31.0 1.8 0.9 0.4 1.1 0.5 7.5 1.1

wildcelery Vallisneria americana Michx. 19.3 1.6 2.1 0.6 1.7 0.6 16.2 1.5

Rooted floating-leaf vegetation

lotus, American Nelumbo lutea Willd. 6.9 1.0 5.8 1.0 11.8 1.6 21.3 1.7

pond-lily, yellow Nuphar variegata Dur. 1.1 0.4 0.2 0.2 0.0 0.0 0.0 0.0

waterlily, white Nymphaea odorata Ait. 12.7 1.3 4.4 0.9 3.0 0.8 5.6 1.0

Emergent vegetation

arrowhead, broadleaf Sagittaria latifolia Willd. 8.2 1.1 2.6 0.7 5.7 1.2 4.5 0.9

arrowhead, stiff Sagittaria rigida Pursh 7.1 1.0 0.5 0.3 0.8 0.4 0.1 0.1

bulrush, river Schoenoplectus fluviatilis (Torr) 

MT Strong 1.1 0.4 0.2 0.2 1.8 0.7 0.4 0.2

bulrush, softstem Schoenoplectus tabernaemontani

(K.C. Gelm) Palla 1.7 0.5 0.0 0.0 0.0 0.0 0.4 0.3

burreed, giant Sparganium eurycarpum Engelm 

x Gray 1.5 0.5 0.0 0.0 0.4 0.3 0.2 0.2

canarygrass, reed Phalaris arundinacea L. 1.6 0.5 0.3 0.2 0.8 0.4 0.5 0.3

cattail, broadleaf Typha latifolia L. 0.0 0.0 0.0 0.0 0.4 0.3 0.0 0.0

cutgrass, rice Leersia oryzoides (L.) Sw. 3.0 0.7 0.3 0.2 2.4 0.8 1.0 0.4

dock Rumex spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.2

loosestrife, purple Lythrum salicaria L. 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.3

pickerelweed Pontederia cordata L. 0.9 0.4 0.0 0.0 0.0 0.0 0.0 0.0

reed, common Phragmites australis (Cav.) Trin. 

ex Steud. 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1

rice, wild Zizania aquatica L. 1.7 0.5 0.0 0.0 0.0 0.0 0.0 0.0

smartweed, Pennsylvania Polygonum pensylvanicum L. 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.2

smartweed, water Polygonum amphibium L. 0.2 0.2 0.0 0.0 0.0 0.0 0.0 0.0

spikerush Eleocharis spp. 0.5 0.3 0.0 0.0 0.0 0.0 0.1 0.1

a

Percent frequency of occurrence

b

Standard error
E-1

Appendix E. Percent frequency of occurrence by species for Pool 26 and Alton Pool 

based on 2002 stratified random sampling, Long Term Resource Monitoring Program, 

Upper Mississippi River System. 

Pool 26

Lower 

Alton Pool

Upper 

Alton Pool

n = 277 n = 140 n = 408

Common name Scientific name Frqa Stdb Frq Std Frq Std

Submersed vegetation

pondweed, leafy Potamogeton foliosus Raf 0.0 0.0 0.8 0.8 0.0 0.0

pondweed, longleaf P. nodosus Poir. 0.0 0.0 0.8 0.8 0.0 0.0

pondweed, sago Stuckenia pectinatus (L.) Boerner 0.2 0.3 3.4 1.5 0.0 0.0

stargrass, water Heteranthera dubia (Jacq.) MacM. 0.0 0.0 1.7 1.1 0.0 0.0

waternymph, southern Najas guadalupensis (Spreng.) Magnus 0.0 0.0 3.4 1.5 0.0 0.0

Rooted floating-leaf vegetation

lotus, American Nelumbo lutea Willd. 0.4 0.4 5.0 1.9 0.0 0.0

primrose-willow, floating Ludwigia peploides (Kunth) Raven 1.2 0.7 0.8 0.8 0.0 0.0

waterhyssop, disk Bacopa rotundifolia (Michx.) Wettst. 0.8 0.5 0.0 0.0 0.0 0.0

Emergent vegetation

amaranth, roughfruit Amaranthus tuberculatus (Moq.) Sauer 0.4 0.4 5.9 2.0 1.2 0.5

arrowhead, arumleaf Sagittaria cuneata Sheldon 0.2 0.3 4.2 1.7 0.0 0.0

arrowhead, broadleaf Sagittaria latifolia Willd. 2.1 0.9 0.8 0.8 0.7 0.4

ash, green Fraxinus pennsylvanica Marsh 0.3 0.3 0.8 0.8 0.4 0.3

barnyardgrass Echinochloa crus-galli (L.) Beauv. 1.1 0.6 7.6 2.2 1.8 0.7

barnyardgrass, rough Echinochloa muricata (Beauv) Fern. 0.3 0.3 0.0 0.0 0.0 0.0

beggarticks, bearded Bidens aristosa (Michx.) Britt. 0.3 0.3 0.0 0.0 0.0 0.0

buttonbush, common Cephalanthus occidentalis L. 1.2 0.7 0.8 0.8 0.1 0.2

bulrush, river Schoenoplectus fluviatilis (Torr) Strong 2.0 0.8 0.0 0.0 0.0 0.0

cockleburr, rough Xanthium strumarium L. 0.3 0.3 2.5 1.3 1.6 0.6

cottonwood, eastern Populus deltoides Bartr. x Marsh. 0.4 0.4 0.8 0.8 0.3 0.3

crabgrass Digitaria spp. 0.0 0.0 2.5 1.3 0.0 0.0

cucumber, oneseed burr Sicyos angulatus L. 0.5 0.4 0.0 0.0 0.0 0.0

cutgrass, rice Leersia oryzoides (L.) Sw. 0.0 0.0 1.7 1.1 0.0 0.0

daisy, false Eclipta prostrata (L.) L. 0.3 0.3 0.0 0.0 0.0 0.0

elm, American Ulmus americana L. 0.0 0.0 0.0 0.0 0.4 0.3

flatsedge, redroot Cyperus erythrorhizos Muhl. 2.3 0.9 5.9 2.0 1.2 0.5

flatsedge, strawcolored Cyperus strigosus L. 0.2 0.3 0.0 0.0 0.0 0.0

dayflower, climbing Commelina diffusa Burm. f. 0.3 0.3 0.0 0.0 0.0 0.0

fogfruit, lanceleaf Phyla lanceolata (Michx.) Greene 1.0 0.6 0.0 0.0 0.0 0.0

grape, graybark Vitis cinerea (Engelm.) Millard 0.0 0.0 0.0 0.0 0.3 0.3

grass, coast cockspur Echinochloa walteri (Pursh) Heller 0.0 0.0 0.8 0.8 0.0 0.0

groundcherry Physalis spp. 0.1 0.2 0.0 0.0 0.0 0.0

lovegrass, tufted Eragrostis pectinacea (Michx.) Nees. ex 

Steud. 0.0 0.0 0.0 0.0 1.2 0.5

maple, silver Acer saccharinum L. 2.6 1.0 0.0 0.0 0.3 0.3

milkweed, swamp Asclepias incarnata L. 1.0 0.6 0.0 0.0 0.0 0.0

nettle, false Boehmeria cylindrica (L.) Sw. 0.1 0.2 1.7 1.1 0.0 0.0

paspalum, horsetail Paspalum fluitans (Ell.) Kunth 0.2 0.3 0.0 0.0 0.0 0.0

persimmon, common Diospyros virginiana L. 0.2 0.3 0.0 0.0 0.0 0.0

rosemallow, halberdleaf Hibiscus laevis All. 0.5 0.4 0.8 0.8 0.0 0.0

rush, common Juncus effuses L. 0.2 0.3 0.0 0.0 0.0 0.0

sedge Carex spp. 0.1 0.2 0.0 0.0 0.0 0.0

smartweed, Pennsylvania Polygonum pensylvanicum L. 0.5 0.4 0.0 0.0 0.1 0.2

smartweed, swamp Polygonum hydropiperoides Michx. 2.9 1.0 2.5 1.3 1.2 0.5

smartweed, water Polygonum amphibium L. 0.0 0.0 0.8 0.8 0.0 0.0

sprangletop, Amazon Leptochloa panicoides (J Presl) AS Hitchc 2.9 1.0 4.2 1.7 1.2 0.5

sprangletop, bearded Leptochloa fusca (L.) Kunth spp. 

fascicularis (Lam.) N. Snow 0.0 0.0 0.8 0.8 0.0 0.0

stonecrop, ditch Penthorum sedoides L. 0.8 0.6 0.0 0.0 0.0 0.0

swampprivet, eastern Forestiera acuminata (Michx.) Poir. 0.0 0.0 0.8 0.8 0.0 0.0

whitestar Ipomoea lacunose L. 0.5 0.4 2.5 1.3 0.0 0.0

willow, black Salix nigra Marsh. 0.3 0.3 0.0 0.0 0.6 0.4 a

Percent frequency of occurrence

b

Standard error
F-1

Appendix F. Percent frequency of occurrence by species for La Grange Pool 

based on 2002 stratified random sampling, Long Term Resource Monitoring Program, 

Upper Mississippi River System. 

La Grange Pool

La Grange 

Floodplain Lakes

n = 369 n = 59

Common name Scientific name Frqa Stdb Frq Std

Submersed vegetation

bladderwort, common Utricularia macrorhiza Le Conte 0.0 0.0 11.9 4.2

chara Chara spp. 0.0 0.0 11.9 4.2

coontail Ceratophyllum demersum L. 0.0 0.0 57.6 6.5

pondweed, curly Potamogeton crispus L. 0.0 0.0 5.1 2.9

pondweed, horned Zannichellia palustris L. 0.0 0.0 6.8 3.3

pondweed, leafy/small P. foliosus Raf./P. L. 0.0 0.0 8.5 3.7

pondweed, longleaf P. nodosus Poir. 0.0 0.0 5.1 2.9

pondweed, sago Stuckenia pectinatus (L.) Boerner 0.0 0.0 6.8 3.3

stargrass, water Heteranthera dubia (Jacq.) MacM. 0.0 0.0 3.4 2.4

watermilfoil, Eurasian Myriophyllum spicatum L. 0.0 0.0 72.9 5.8

watermilfoil, northern M. sibiricum Komarov 0.0 0.0 10.2 4.0

waternymph, brittle Najas minor All. 0.0 0.0 8.5 3.7

waternymph, nodding N. flexilis (Willd.) Rostk. & Schmidt 0.0 0.0 10.2 4.0

Rooted floating—leaf vegetation

lotus, American Nelumbo lutea Willd. 1.9 0.7 25.4 5.7

primrose-willow, wingleaf Ludwigia decurrens Walt. 0.3 0.3 0.0 0.0

waterlily, white Nymphaea odorata Ait. 0.0 0.0 13.6 4.5

Emergent vegetation

arrowhead, broadleaf Sagittaria latifolia Willd. 0.4 0.3 0.0 0.0

millet, Japanese Echinochloa esculenta (Braun) H Scholz 2.1 0.8 0.0 0.0 a

Percent frequency of occurrence

b

Standard error
REPORT DOCUMENTATION PAGE Form Approved

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Washington, D.C. 20503

1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE

January 2005

3. REPORT TYPE AND DATES COVERED

4. TITLE AND SUBTITLE Multiyear synthesis of the aquatic vegetation component from 1991 to 2002 for the Long Term 

Resource Monitoring Program

5. FUNDING NUMBERS

6. AUTHOR(S) Yao Yin1 and Heidi Langrehr2

7. PERFORMING ORGANIZATION NAME AND ADDRESS

1

U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603

2

Wisconsin Department of Natural Resources, LTRMP Onalaska Field Station, 2630 Fanta Reed Road, La Crosse, Wisconsin, 

54603

8. PERFORMING ORGANIZATION

 REPORT NUMBER

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES)

 U.S. Geological Survey 

 Upper Midwest Environmental Sciences Center

 2630 Fanta Reed Road

 La Crosse, Wisconsin, 54603

10. SPONSORING/MONITORING

 AGENCY REPORT NUMBER

 2005-T001

11. SUPPLEMENTARY NOTES

12a. DISTRIBUTION/AVAILABILITY STATEMENT

Release unlimited. Available from National Technical Information Service, 5285 Port Royal Road, Springfield, 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).

12b. DISTRIBUTION CODE

13. ABSTRACT (Maximum 200 words) 

Aquatic vegetation data were collected in the Upper Mississippi River System (UMRS) under the Long Term Resource Monitoring Program (LTRMP). From 1991 to 2002, 

five reaches were surveyed every year (key pools), and another five reaches were surveyed once (outpools). The study design changed from a protocol involving sampling 

along transects (1991–2000) to a protocol incorporating stratified random sampling (1998–2002) with concurrent sampling under both protocols in 1998–2000. The frequency 

of occurrence of plants revealed no synchronous trends among three key pools (Pools 4, 8, and 13) supporting sizable submersed aquatic vegetation beds. Submersed aquatic 

vegetation in upper Pool 4 declined steadily between 1991 and 2002. Submersed aquatic vegetation in lower Pool 4 declined between 1991 and 1996 and thereafter recovered 

moderately. Submersed aquatic vegetation in Pool 8 increased between 1991 and 1999, which probably was a recovery process from a reported sudden collapse after the 1987–

1989 drought. Submersed aquatic vegetation in Pool 13 demonstrated a high degree of stability during the period of monitoring despite drastic fluctuations between spring and 

summer sampling in some years. Water turbidity and water level fluctuation were strongly correlated with the longitudinal pattern of submersed aquatic vegetation distribution 

in the UMRS. Pools with clearer water and less fluctuating water levels supported more submersed aquatic vegetation. The LTRMP key pools represented a wide spectrum of 

the UMRS habitats. The habitat rehabilitation and enhancement project (HREP) at Stoddard Bay in Pool 8 effectively stimulated colonization by aquatic vegetation.

14. SUBJECT TERMS

Aquatic vegetation, rooted floating-leaf, Illinois River, key pools, Long Term Resource Monitoring Program, Upper Mississippi 

River, outpools, submersed vegetation 

15. NUMBER OF PAGES

29 pp. + Appendixes A–F.

16. PRICE CODE

17. SECURITY CLASSIFICATION

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18. SECURITY CLASSIFICATION

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19. SECURITY CLASSIFICATION

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20. LIMITATION OF ABSTRACT
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.