Long Term Resource Monitoring Program

Technical Report 

2005-T003

March 2005

Multiyear Synthesis of Limnological Data

from 1993 to 2001

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 Limnological Data

from 1993 to 2001

for the Long Term Resource Monitoring Program

Edited by

Jeffrey N. Houser

Contributing Authors

David W. Bierman, Robert M. Burdis, James R. Fischer, James T. Rogala,

Lori A. Soeken-Gittinger, Kraig L. Hoff, and Erik Harms

Final Report submitted to

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

Clock Tower Building

PO Box 2004

Rock Island, Illinois 61204-2004

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

March 2005
Suggested citation:

Houser, J. N., editor. 2005. Multiyear synthesis of limnological data from 1993 to 2001 for the Long Term Resource Monitoring Program. Final report submitted to the U.S. Army Corps of Engineers from the U.S. Geological Survey, Upper Midwest 

Environment Sciences Center, La Crosse, Wisconsin, March 2005. LTRMP Technical Report 2005-T003. 59 pp.

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

Executive Summary

This report presents a broad overview of spatial and temporal variation in the limnological 

characteristics of the Upper Mississippi River System (UMRS). Important sources of variability 

within the UMRS include a longitudinal (north–south) gradient, and differences among years, 

seasons, and aquatic areas (e.g., main channel versus contiguous backwaters). Understanding spatial 

and temporal variation at these scales requires a systemic perspective on the river. The Long Term 

Resource Monitoring Program (LTRMP) provides a systemic perspective through the collection 

and analysis of monitoring data from six study reaches representing the upper, lower, and open river 

reaches of the UMRS: Pool 4 near Lake City, Minnesota; Pool 8 near Onalaska, Wisconsin; Pool 13 

near Bellevue, Iowa; Pool 26 near Alton, Illinois; and Open River, near Cape Girardeau, Missouri; 

and La Grange Pool of the Illinois River near Havana, Illinois. This report presents data from 1993 to 

2001 (or 2002 when available). The focus is on spring and summer conditions because spring is the 

time of maximum discharge and, therefore, maximum transport of suspended solids and nutrients and 

summer is the time of peak biological activity. Winter data are included in the analyses of dissolved 

oxygen because dissolved oxygen may be a critical component of winter habitat for many fish species 

within the northern reaches of the UMRS.

Discharge is an important driver of physical, chemical, and biotic conditions in large river systems 

such as the UMRS. Discharge determines longitudinal transport of dissolved and particulate 

constituents and is correlated with water surface elevation that determines the degree of connection 

among habitats within the UMRS. Discharge from 1993 to 2001 was variable among reaches and 

years, but general patterns were evident. In most years, maximum discharge was observed in spring 

and early summer with an occasional secondary peak in fall. In the southern reaches, maximum 

discharge between 1993 and 2001 was observed during the 1993 flood; in the northern reaches, 

maximum discharge was observed in spring 2001. Discharge generally was low in 2000, particularly 

in the northern reaches of the UMRS.

Limnological characteristics determine water quality and affect aquatic habitat availability in 

the UMRS. Turbidity and suspended solids and, to a lesser extent, chlorophyll a, are the primary 

determinants of light penetration and, therefore, may affect the distribution of aquatic vegetation. 

In addition, chlorophyll a, an indicator of phytoplankton abundance, serves as a measure of one 

component of biotic production at the base of the food web. Dissolved nutrients are necessary for 

vegetation and phytoplankton growth, but excess nutrients can cause noxious algal blooms which 

can reduce dissolved oxygen concentrations. Sufficient concentration of dissolved oxygen (DO) is a 

critical aspect of habitat suitability for many species of fish. 

Spatial patterns in turbidity, total suspended solids, and chlorophyll a concentrations were 

apparent within the UMRS. There were distinct longitudinal patterns in turbidity and suspended 

solids concentrations; both were much lower in lower Pool 4 than in upper Pool 4 because of the 

trapping of sediments by Lake Pepin. Turbidity and suspended solids increased in each of the study 

reaches from lower Pool 4 to Open River. There were not clear longitudinal patterns in chlorophyll 

a concentrations, but there were spatial patterns within study reaches. For example, chlorophyll 

a concentrations were generally higher in the contiguous backwaters (hereafter referred to as 

backwaters) than in the main channel. 

There were no clear longitudinal patterns in dissolved nutrients, but there were differences among 

aquatic areas within study reaches. Spring nitrate + nitrite (NOx) concentrations varied substantially 

among years, but all of the UMRS study reaches exhibited markedly similar NOx concentrations in 

any given year. The differences among years appeared to be driven by discharge. Low discharge years 

generally exhibited low NOx concentrations. Within study reaches, summer NOx is generally lower 

in backwaters than in the main channel. This was probably because of uptake by primary producers 

(phytoplankton and aquatic vegetation) and dinitrification combined with limited delivery of NOx
iv

to backwaters in low summer flows. La Grange Pool of the Illinois River usually exhibited notably 

higher dissolved nutrient concentrations than did any study reaches of the Upper Mississippi River. 

Seasonal patterns in total suspended solids (TSS), turbidity, chlorophyll a, and nutrient 

concentrations were evident. Turbidity, TSS, and chlorophyll a minima usually occurred in winter. 

In the northern study reaches (4, 8, and 13), winter turbidity and TSS were particularly low and 

exhibited little variation. Seasonal chlorophyll a concentrations in main channels and backwaters 

show peaks in late summer and fall, with minima in winter and early summer. An exception to this 

pattern is the backwaters of La Grange Pool, where chlorophyll a concentrations remained elevated 

from April through September. Contrasting seasonal patterns were seen for dissolved nitrogen and 

phosphorus. Main channel soluble reactive phosphorus (SRP) concentrations peaked in September 

and exhibited minima in April and May; main channel and backwater NOx concentrations exhibited 

minima in fall when SRP concentrations are at their maximum. 

There were not strong longitudinal trends in DO concentrations, although there were differences 

among study reaches. Seasonal DO patterns differed slightly among the northern (Pools 4, 8, and 13) 

and southern (Pool 26, Open River, La Grange Pool) study reaches. In the northern study reaches, 

DO concentrations are generally highest in spring, lowest in summer and winter, and intermediate in 

fall. In the southern study reaches, DO concentrations are highest in winter, lowest in summer, and 

intermediate in spring and fall. The overall occurrence of low, daytime, surface DO concentration 

was infrequent in UMRS (about 4% of the sites monitored were <5 mg/L); however, during certain 

seasons and in certain areas, low surface DO did occur. Low DO on the Upper Mississippi River was 

most frequently observed in summer (12–21% of backwater sampling sites in Pools 8, 13, and 26) 

followed by winter (10–14% of backwater sites in Pools 4, 8, and 13) and was regularly observed 

only in backwater areas. In La Grange Pool, low summer DO occurred regularly in the main (25% of 

sites sampled) and side channel (35% of sites sampled) areas.

Spatial patterns in conductivity were used to examine the spatial extent of tributary influence on the 

UMRS. The effects of tributary inputs on spatial patterns in conductivity in the UMRS vary greatly 

among tributaries because of differences in discharge among tributaries and annual and seasonal 

hydrologic variations in the LTRMP study reaches. Of the six LTRMP study reaches, Pools 4, 8, 

and 26 showed clear spatial patterns in conductivity related to tributary input in some years whereas 

Pool 13, Open River, and La Grange Pool did not. The effect of tributaries on the spatial patterns in 

specific conductivity varied from year-to-year most likely because of differences in tributary and river 

discharge. There were no obvious effects of tributaries on spatial patterns in total phosphorus (TP), 

total nitrogen (TN), or TSS.

Three studies of the relation among sampling sites in the backwaters, tributaries, and main channels 

suggest that concentrations of TP, TN, and TSS at backwater sampling sites were correlated with 

concentration at both tributary and main channel sites. However, concentrations at the backwater sites 

were more strongly correlated with concentrations at the main channel sites than with concentrations 

at the tributary sites.

The patterns described here suggest possible processes that affect water quality in the UMRS. 

Additional analyses and specifically designed studies are needed to better understand the processes 

creating the patterns described here. Specific recommendations for additional analyses are presented 

in individual chapters.
v

Contents

Executive Summary ....................................................................................... iii

Preface ......................................................................................................... xi

Chapter 1: Introduction .................................................................................... 2

Chapter 2: Hydrology ....................................................................................... 4

Background ............................................................................................. 4

Methods ................................................................................................ 4

Results ................................................................................................... 5

Chapter 3: Spatial Patterns in Suspended Solids, Turbidity, and Chlorophyll a ..................... 11

Background ............................................................................................. 11

Methods ................................................................................................ 11

Results ................................................................................................... 11

Longitudinal Patterns in Summer Concentrations of Suspended Solids and

Chlorophyll a .............................................................................. 11

Longitudinal and Seasonal Patterns in Turbidity and Chlorophyll a ........................14

Habitat and Management Implications ............................................................ 14

Chapter 4: Seasonal and Annual Variation in Nitrogen, Phosphorous, and Chlorophyll a ...... 20

Background ............................................................................................. 20

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

Results and Discussion .............................................................................. 21

Annual Patterns ................................................................................. 21

Seasonal Patterns ................................................................................. 24

Conclusions ............................................................................................. 25

Chapter 5: Spatial and Temporal Variation of Dissolved Oxygen .................................... 28

Background ............................................................................................. 28

Methods ................................................................................................ 28

Results and Discussion .............................................................................. 29

Seasonal Means by Study Reaches ............................................................ 29

Summary of Seasonal Patterns .................................................................. 29

Spatial Patterns in Low DO Concentrations ................................................... 34

Areal Extent of Low DO Concentrations ...................................................... 35

Summer ....................................................................................... 35

Winter ....................................................................................... 35

Summary ................................................................................................ 37

Chapter 6: Tributaries and Their Influence on Water Quality Spatial Patterns ..................... 39

Background ............................................................................................. 39

Methods ................................................................................................ 40

Patterns in Tributary Conductivity ............................................................ 40

Tributary Influences on Backwaters ............................................................ 40

Longitudinal Tributary Trends .................................................................. 40

Results and Discussion .............................................................................. 41

Spatial Patterns in Specific Conductivity ................................................... 41

Page
vi

Page

Number

Pool 4 ....................................................................................... 41

Pool 8 ....................................................................................... 41

Pool 13 ....................................................................................... 41

Pool 26 ....................................................................................... 41

Open River ................................................................................. 41

La Grange Pool of the Illinois River ................................................... 42

Total Nitrogen, Total Phosphorus, and Total Suspended Solids ..................... 43

Water Quality Comparison of Sampling Sites in Backwater, Tributary, and

Main Channel Areas ..................................................................... 45

Galena River/Sunfish Lake and Rush Creek/Savanna Bay ........................... 46

Rock Creek/Shrickers Lake ............................................................... 52

Water Quality in Tributaries of the Upper Mississippi and Illinois Rivers ............... 52

Upper Mississippi River Tributaries ...................................................... 54

Illinois River Tributaries .................................................................. 55

Summary ................................................................................................ 55

References ................................................................................................... 56

Tables

2.1. U.S. Geological Survey (USGS) gaging stations selected to represent the

Long Term Resource Monitoring Program (LTRMP) study reaches ........................ 4

2.2. Mean and standard deviation (SD) for discharge (cfs) from the 9-year sampling period

for each study reach by season ..................................................................... 6

2.3. Discharge conditions relative to mean discharge (1993–2001) by season and by

study reach for the 9-year study period ............................................................ 8

5.1. Mean proportion of stratified random sampling sites with dissolved oxygen

concentration <5 mg L-1 in winter and summer from 1993 to 2001 ........................... 35

6.1. Mean conductivity (μS/cm) for study reaches and selected tributaries in the

Upper Mississippi and Illinois Rivers, 1993–2001 ............................................. 45

6.2. Baseflow discharge and mean concentrations of total nitrogen (TN), total phosphorus

(TP), total suspended solids (TSS), and turbidity for selected tributaries based on

fixed-site sampling by the Long Term Resource Monitoring Program in 1993–2001 ...... 54
vii

Figures

1.1. Study reaches monitored in the Upper Mississippi River System by the Long

Term Resource Monitoring Program field stations ............................................. 3

2.1. Daily discharge (cfs) for the nearest U.S. Geological Station gaging station for each

of the six Long Term Resource Monitoring Program study reaches, 1993–2001 ............ 5

2.2. Standardized seasonal annual mean discharges for the six gages near the Long

Term Resource Monitoring Program study reaches during the 9-year sampling

period (1993–2001) ................................................................................. 7

2.3. Standardized seasonal annual mean discharges for the six gages near the Long

Term Resource Monitoring Program study reaches during the 9-year sampling

period (1993–2001) ................................................................................. 9

2.4. Yearly seasonal mean discharge (cfs) at Clinton, Iowa, for a 128-year period

(1874–2001) .......................................................................................... 10

3.1. (A) Mean total suspended solids (mg/L), (B) volatile suspended solids (mg/L), 

(C) percent volatile suspended solids, (D) inorganic suspended solids (mg/L), and

(E) chlorophyll a (μg/L) in the main channel and backwaters in the Long Term

Resource Monitoring Program (LTRMP) study reaches during summer stratified

random sampling .................................................................................... 13

3.2. Box plots of winter, spring, summer, and fall turbidity (in nephelometric turbidity

units [NTU]) in (A) main channel and (B) backwaters in the Long Term Resource 

Monitoring Program study reaches during stratified random sampling from 1993

through 2001 .......................................................................................... 15

3.3. Box plots of winter, spring, summer and fall chlorophyll a concentrations (μg/L) in

(A) main channel and (B) backwaters in the Long Term Resource Monitoring Program

study reaches during stratified random sampling from 1993 through 2001 .................. 16

3.4. Correlation between mean discharge (cfs) and mean chlorophyll a (μg/L) in the

main channel and backwaters in the Long Term Resource Monitoring Program study

reaches ([A] upper Pool 4, [B] lower Pool 4, [C] Pool 8, [D] Pool 13, [E] Pool 26,

[F] Open River, and [G] La Grange Pool) during summer stratified random sampling

(1993–2001) .......................................................................................... 18

4.1. Annual means of soluble reactive phosphorous (mg/L), nitrate + nitrite oxygen

(mg/L; NOx), and chlorophyll a (μg/L) in the main channel and backwaters

of the Upper Mississippi and Illinois Rivers based on spring stratified random

sampling (SRS) from 1994 to 2002 ............................................................... 22

4.2. Annual means of soluble reactive phosphorous (mg/L), nitrate + nitrite nitrogen

(mg/L; NOx), and chlorophyll a (μg/L) in the main channel and backwaters of the

Upper Mississippi and Illinois Rivers based on summer stratified random sampling

(SRS) from 1993 to 2002 ........................................................................... 23

4.3. Monthly mean (1993–2001) soluble reactive phosphorous (mg/L) concentrations

in the main channel and backwaters of the Upper Mississippi and Illinois Rivers ......... 25

4.4. Monthly mean (1993–2001) nitrate + nitrite (mg/L; NOx) concentrations in the

main channel and backwaters of the Upper Mississippi and Illinois Rivers .................. 26

4.5. Monthly mean (1993–2001) chlorophyll a concentrations (μg/L) in the main channel

and backwaters of the Upper Mississippi and Illinois Rivers ................................. 27

Number Page
viii

5.1. Spring dissolved oxygen (DO) in all strata of the six study reaches based on the

Long Term Resource Monitoring Program stratified random sampling data,

1994–2002 ............................................................................................. 30

5.2. Summer dissolved oxygen (DO) in all strata of the six study reaches based on the

Long Term Resource Monitoring Program stratified random sampling data, 

1993–2002 ............................................................................................. 31

5.3. Fall dissolved oxygen (DO) in all strata of the six study reaches based on the Long Term

Resource Monitoring Program stratified random sampling data, 1993–2002 ............... 32

5.4. Winter dissolved oxygen (DO) in all strata of the six study reaches based on the

Long Term Resource Monitoring Program stratified random sampling data, 

1994–2002 ............................................................................................. 33

5.5. Dissolved oxygen (DO) saturation versus average snow and ice depth for the backwaters

of the Long Term Resource Monitoring study reaches, 1994–2002 ........................... 34

5.6. Extent of low dissolved oxygen (DO) concentration (<5 mg/L) observed in summer 

stratified random sampling in backwaters of the Long Term Resource Monitoring

Program study reaches, 1993–2001 ............................................................... 36

5.7. Extent of low dissolved oxygen (DO) concentration (<5 mg/L) observed in winter

stratified random sampling in backwaters of the Long Term Resource Monitoring

Program study reaches, 1994–2001 ............................................................... 37

6.1. Local influence of the Chippewa River on water quality of lower Pool 4, based upon

specific conductivity (μS/cm) readings from summer stratified random sampling ......... 42

6.2. Local influence of the Black River on water quality in the eastern half of Pool 8, based

upon specific conductivity (μS/cm) from summer stratified random sampling ............... 43

6.3. Local influence of the Illinois River on main channel water quality of Pool 26, based

on specific conductivity (μS/cm) from summer stratified random sampling .................. 44

6.4. Pool 12 of the Upper Mississippi River showing the Lock and Dam 11 tailwater site, 

Sunfish Lake site, and the Galena River ......................................................... 46

6.5. Pool 13 of the Upper Mississippi River showing the Lock and Dam 12 tailwater site,

 Savanna Bay site, and Rush Creek ............................................................... 47

6.6. Pool 14 of the Upper Mississippi River showing Pool 14 main channel border fixed-site 

sampling, Shrickers Lake site, and Rock Creek ................................................ 48

6.7. Scatter plots with Spearman correlation values for total nitrogen (mg/L) at backwater,

main channel, and tributary sites .................................................................. 49

6.8. Scatter plots with Spearman correlation values for total phosphorus (mg/L) at

backwater, main channel, and tributary sites ...................................................... 50

6.9. Scatter plots with Spearman correlation values for total suspended solids (mg/L) at

backwater, main channel, and tributary sites ...................................................... 51

6.10. Longitudinal patterns in total nitrogen (mg/L), total phosphorus (mg/L), total 

suspended solids (mg/L), and turbidity (nephelometric turbidity units [NTU]) in

selected tributaries to, and main channels of, the six Long Term Resource Monitoring

Program study areas, based on overall means from 1993 to 2001 .............................. 53

Number Page
ix

Preface

The Long Term Resource Monitoring Program (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 as 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 multipleuse 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 multiyear report supports Task 2.2.3 as specified in Goal 2, Monitor Resource Change, of 

the LTRMP Operating Plan (U.S. Fish and Wildlife Service 1993). This report was developed with 

funding provided by the LTRMP.
Multiyear Synthesis of Limnological Data

from 1993 to 2001

for the Long Term Resource Monitoring Program 

Edited by Jeffrey N. Houser1

Contributing Authors

David W. Bierman2, Robert M. Burdis3, James R. Fischer4, James T. Rogala1,

Lori A. Soeken-Gittinger5, Kraig L. Hoff4, and Erik Harms4

1

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

2630 Fanta Reed Road, La Crosse, Wisconsin 54603

2

Iowa Department of Natural Resources, Mississippi River Monitoring Station

206 Rose Street, Bellevue, Iowa 52031

3

Minnesota Department of Natural Resources, Lake City Field Station

1801 S. Oak Street, Lake City, Minnesota 55041

4

Wisconsin Department of Natural Resources, Pool 8 Field Station

2630 Fanta Reed Road, La Crosse, Wisconsin 54603

5

Illinois Natural History Survey, Pool 26 Field Station

8450 Montclair, Brighton, Illinois 62012

Abstract: This report presents a broad overview of spatial and temporal variation in the water quality of 

the Upper Mississippi River System (UMRS). The Long Term Resource Monitoring Program (LTRMP) 

provides a systemic perspective through the collection and analysis of monitoring data from six study reaches 

representing the upper, lower, and open river reaches of the UMRS (Upper Mississippi River:

Pools 4, 8, 13, and 26, Open River [near Cape Girardeau, Missouri]; Illinois River: La Grange Pool). 

This report presents data from 1993 to 2001 (or 2002 when available) and focuses on spring and summer 

conditions. Water quality constituents (e.g., turbidity, suspended solids, chlorophyll, nutrients, and dissolved 

oxygen) varied among study reaches, aquatic area (e.g., main channel, contiguous backwaters, etc.) and 

seasons. For example, turbidity and suspended solids varied substantially among pools. Turbidity and 

suspended solids were much lower in lower Pool 4 than in upper Pool 4 because of the trapping of sediments 

by Lake Pepin, but increased in each of the study reaches from Pool 4 to Open River. Chlorophyll a and 

nutrient concentrations often differed between the main channel and contiguous backwater areas (hereafter 

referred to as backwaters). Summer chlorophyll a concentrations were generally higher in backwaters than in 

the main channel, and summer nitrate + nitrite (NOx) concentrations were generally lower in backwaters than 

in the main channel. Seasonal patterns were evident in chlorophyll a, nutrient, and dissolved oxygen (DO) 

concentrations. Main channel soluble reactive phosphorus (SRP) concentrations peaked in September and 

exhibited minima in April and May. In contrast, main channel and backwater NOx concentrations exhibited 

minima in fall when SRP concentrations are at their maximum. Seasonal chlorophyll a concentrations in 

main channels and backwaters show peaks in late summer and fall, with minima in winter and early summer. 

Seasonal DO patterns differed slightly among the northern (Pools 4, 8, and 13) and southern (Pool 26, 

Open River, La Grange Pool) study reaches. In the northern study reaches, DO concentrations are generally 

highest in spring, lowest in summer and winter, and intermediate in fall. In the southern study reaches, DO 

concentrations are highest in winter, lowest in summer, and intermediate in spring and fall. Spatial patterns 

within study reaches caused by tributary inputs were shown by the spatial patterns in specific conductivity. 

Of the six LTRMP study reaches, Pools 4, 8, and 26 showed clear spatial patterns in conductivity related to 

tributary input in some years whereas Pool 13, Open River, and La Grange Pool did not.

Key words: dissolved oxygen, ecosystem monitoring, hydrology, Mississippi River, nitrate, nitrogen, 

phosphorus, spatial patterns, suspended solids, temporal patterns
2

Rivers ecosystems are highly heterogeneous in 

time and space. Our understanding of what drives 

this heterogeneity is poor. Because of its systemic 

perspective, the Long Term Resource Monitoring 

Program (LTRMP) is well suited to improve 

our understanding of this temporal and spatial 

heterogeneity in the Upper Mississippi River 

System (UMRS). Important sources of variability 

in water quality include the longitudinal (north–

south) gradient and differences among years, 

seasons, and aquatic areas.

A number of important drivers of river water 

quality change along the north–south gradient of 

the UMRS. Climatic conditions differ between 

the northern and southern reaches of the UMRS. 

For example, winters are longer and colder in 

the northern reaches. The river is affected by the 

tributaries that enter it as it flows south (Wasley 

2000). Geomorphology and land use in the basin 

also change along a north–south gradient. The 

proportion of the floodplain used for agriculture 

increases moving from north to south (Yin 1998), 

and levees become more extensive. To what 

extent are these changes in geomorphology and 

land use reflected in river water quality?

There are also likely to be spatial patterns in 

water quality at a smaller scale because of the 

broad range of geomorphic characteristics in 

the river. For example, main channel areas are 

characterized by deeper water and faster current 

velocities than are backwater areas. The LTRMP 

uses a sampling design stratified across the 

geomorphic units (referred to as strata in this 

report) to accommodate the variation among 

different geomorphic areas in the UMRS (Soballe 

and Fischer 2004). 

There is temporal variation in the water 

quality of the UMRS because of seasonal and 

interannual differences. Differences among 

years may be driven by year-to-year differences 

in precipitation and temperature. Trends across 

many years may be driven by long-term changes 

in climate or land use. Seasonal patterns may be 

driven by seasonal differences in discharge, solar 

irradiation, precipitation, evapotransporation, 

and temperature. What effect does seasonality in 

these drivers have on river water quality?

The design of the monitoring program was 

modified substantially in 1993, and this report 

covers data from 1993 through 2001 or 2002 

depending on data availability at the time of 

analysis. Soballe and Fischer (2004) provide 

detailed information concerning the LTRMP 

field sampling and laboratory procedures; only 

a brief discussion is included here (an electronic 

copy of Soballe and Fischer [2004] and all of the 

LTRMP water quality data are available online 

at http://www.umesc.usgs.gov/data_library/

water_quality/water_quality_page.html). To 

gain a systemic perspective on the UMRS, six 

study reaches representing the upper, lower, 

and open river reaches of the UMR and the 

lower Illinois River are monitored by LTRMP: 

Pool 4 near Lake City, Minnesota (river mile 

753 to 797); Pool 8 near Onalaska, Wisconsin 

(river mile 679 to 702.5); Pool 13 near Bellevue, 

Iowa (river mile 522.5 to 557); Pool 26 near 

Alton, Illinois (river mile 203 to 241.5); Open 

River near Cape Girardeau, Missouri (river mile 

29 to 80); and La Grange Pool of the Illinois 

River near Havana, Illinois (river mile 80 to 

158; Figure 1.1). The LTRMP water quality 

component uses two complimentary sampling 

programs: fixed-site and stratified random 

sampling. The fixed-site sampling monitors 

inflows, outflows, selected tributaries, and other 

areas of special interest at a limited number of 

sites (13–15) in each study reach at biweekly or 

monthly intervals. The relatively high temporal 

resolution of the fixed-site data makes it useful to 

examine seasonal patterns. However, the fixedsite data are not suitable for making inferences 

about strata or study reaches because of the 

subjective criteria used for their selection. 

Stratified random sampling is more limited 

in temporal resolution, conducted in four 

Chapter 1: Introduction

by

Jeffrey N. Houser
3

quarterly episodes each year, but is at a much 

higher spatial resolution. The SRS sampling 

began in summer 1993 for Pools 4, 8, and 13 

and La Grange Pool and began in fall 1993 

for Pool 26 and Open River. Each quarterly 

sampling episode is generally completed in 

10 to 14 days. The spring episode begins the 

last week of April, the summer episode begins 

the last week of July, the fall episode begins 

the second week of October, and the winter 

Figure 1.1. Study reaches monitored in the Upper Mississippi River 

System by the Long Term Resource Monitoring Program field stations.

episode begins the last week of January. 

Between 135 and 150 sampling sites are 

randomly selected from six strata. The 

sampling strata are based on geomorphic 

characteristics as described in Wilcox 

(1993) and included the following: 

main channel, side channel, impounded 

areas, contiguous backwaters, and 

isolated backwaters. This report focuses 

on data from contiguous backwaters 

(hereafter referred to as backwaters) 

and the main channel because they 

represent an informative contrast in both 

depth and current velocity. The main 

channel is deep and has high current 

velocity; backwaters are generally 

shallow and have low current velocity. 

Other common types of aquatic areas 

in the river include side channels 

and impoundments that are generally 

intermediate in both depth and current 

velocity. Details concerning the 

distribution of sampling effort among 

these aquatic areas can be found in 

Soballe and Fischer (2004, Table 3). 

The main objective of this multiyear 

report is to provide a summary of the 

patterns observed in the UMRS for 

selected water quality variables from 

1993 to 2001 (or 2002 when available). 

The report focuses on various aspects of temporal 

and spatial variability in selected water quality 

parameters in the UMRS. The specific aspects 

addressed include (1) differences among study 

reaches; (2) differences among geomorphic 

strata (e.g., main channel, backwaters); and 

(3) temporal patterns including differences 

among years and seasonal patterns. 
4

Background

Discharge is an important driver of physical, 

chemical, and biotic conditions in large river 

systems such as the Upper Mississippi River 

System (UMRS). Discharge determines 

longitudinal transport of dissolved and particulate 

constituents, and these constituents are important 

determinants of habitat conditions. Discharge 

is correlated with water surface elevation 

which determines the degree of connection 

among habitats within the UMRS. When 

water elevations are high, lateral transport 

occurs among the main channel, off-channel 

and terrestrial areas. Thus, discharge provides 

a measure of lateral transport (i.e., channel 

materials delivered to off-channels and terrestrial 

areas), as well as a measure of habitat conditions 

(e.g., water depth). Physical energy is also a 

function of discharge; thus, discharge affects the 

movement of bed materials, and high discharge 

can affect biotic components (e.g., aquatic plant 

breakage).

A summary of discharge conditions in 1993 to 

2001 provides context for the observed patterns 

in limnological characteristics. In addition, the 

9-year sampling period is placed into a larger 

temporal context using historical discharge data. 

Methods

Daily discharge data were acquired from 

the U.S. Geological Survey gaging stations 

(U.S. Geological Survey 2003) closest to the 

six Long Term Resource Monitoring Program 

(LTRMP) study reaches (Table 2.1). Only 

gaging stations were used that had been in 

operation at the time of impoundment in the 

1930s and had discharge records through the 

entire LTRMP sampling period of 1993 to 2001. 

The only gap in these discharge records was 

for the Kingston, Illinois gage, where recording 

Chapter 2: Hydrology

by

James T. Rogala

ended in September 2001. Means and standard 

deviations by study reach and year were 

calculated from daily data for the following 

seasons: (1) winter—previous December 

through February, (2) spring—March through 

May, (3) summer—June through August, and 

(4) fall—September through November.

The results below are focused on annual 

patterns of discharge within each reach by 

season. Because the interest is mainly in 

interannual patterns in discharge within each 

study reach for each season, the data were 

standardized by study reach for each season 

in two distinct ways. First, the discharge data 

were standardized to the 1993–2001 mean 

to emphasize differences within the LTRMP 

sampling period. This provides for comparisons 

that are relevant when addressing differences 

in water quality values observed in the LTRMP 

sampling period. The discharge data were also 

standardized to a long-term (60-year) mean 

representing the period of impoundment to 

illustrate how the sampling period compares 

to past discharge conditions. In both these 

examples, the data were standardized by setting 

the mean for each reach and season during the 

period of comparison (9 or 60 years) equal to 

zero, and the standard deviation for each reach 

and season during the period of comparison to 

one. 

Table 2.1. U.S. Geological Survey (USGS) gaging stations 

selected to represent the Long Term Resource Monitoring 

Program (LTRMP) study reaches (see Figure 1.1).

LTRMP sampling reach USGS gaging station

Pool 4 Prescott, Minnesota

Pool 8 Winona, Minnesota

Pool 13 Clinton, Iowa

Pool 26 Grafton, Illinois

Open River Thebes, Missouri

La Grange Pool Kingston, Illinois
5

Results

The annual hydrograph is variable among study 

reaches and years; however, general patterns 

are evident. In most years, maximum discharge 

was observed in spring and early summer 

(Figure 2.1), with an occasional secondary peak 

in fall. The highest discharge over the 9-year 

sampling period occurred during the 1993 

flood, which in addition to the high discharge, 

was unusual in that it extended much later into 

summer than is typical for the Upper Mississippi 

River. 

Seasonal patterns in discharge can also be 

observed by comparing seasonal means for each 

study reach (Table 2.2). Discharge was highest 

in spring for all study reaches, with summer 

discharge being the next highest (ranging from 

70% to 90% of the spring discharge) for all study 

reaches. In the northern three study reaches, 

discharge was higher in fall than winter, whereas 

fall discharge was similar to winter discharge in 

Pool 26 and Open River. Winter discharges were 

higher than fall discharges in La Grange Pool. 

Discharge for all seasons increased with location 

downstream in the Upper Mississippi River. 

Figure 2.1. Daily discharge (cfs) for the nearest U.S. Geological Station gaging station for each of the six 

Long Term Resource Monitoring Program study reaches, 1993–2001. Note that the y-axis differs among study 

reaches.
6

These overall patterns can be used to interpret 

the standardized discharge data and to assess the 

annual discharge conditions in the 9-year study 

period.

The standardized discharge data illustrate 

seasonal patterns across years for each study 

reach. First, the differences were summarized 

among study reaches, as observed as differences 

along the y-axis, within years by season using 

discharge standardized to the 1993–2001 mean. 

In some years, conditions within seasons were 

similar among all study reaches, such as the high 

discharge in summer 1993 and the low discharge 

conditions in spring 2000 (Figure 2.2). However, 

in other years, there were differences in discharge 

patterns among the study reaches. For example, 

discharge was high relative to other years in only 

the northern three study reaches (Pools 4, 8, and 

13) in winter 1993. Figure 2.2 can also be used to 

look for trends over the study period. In general, 

fall discharge steadily decreased from 1993 

to 2001 but no trend is apparent for any other 

season.

To simplify the summary of annual discharge 

conditions across seasons, years of extreme 

discharge were identified on the basis of the 

standard deviation from the 9-year mean, by 

season within study reaches (Table 2.3). Despite 

the differences among study reaches, several 

annual patterns are evident across study reaches. 

Discharge was high in 1993 across all seasons, 

and highest in 1993 for all three southern study 

reaches (Pool 26, Open River, and La Grange 

Pool). Discharge was low in 2000, particularly in 

winter and spring. 

Discharge data standardized to the 60-year 

mean show that yearly seasonal discharge tended 

to be above the historical mean in winter, spring, 

and summer for most years and study reaches, 

whereas fall discharge during the study period 

was below the historical mean for the latter 

years of the study period (Figure 2.3). Discharge 

recorded since 1874 at the Clinton, Iowa, gage 

suggests that the recent 60-year period may be 

on the rising limb of a large-scale pattern for 

all seasons (Figure 2.4). A similar pattern was 

reported by Knox (2000), where large floods 

were found to be more common in the late 1800s 

and since about 1950. Knox (2000) also suggests 

that large-scale atmospheric circulation patterns 

play a large role in this pattern, as well as largerscale patterns in Holocene floods.

In summary, the period 1993–2001 was one of 

relatively high discharge on both 60- and 140-

year scales. The most striking hydrologic event 

in this 9-year period was the 1993 flood. At the 

other end of the spectrum, 2000 was the driest 

year, particularly in winter and spring. These two 

contrasting hydrologic events may provide useful 

comparisons in analyses of ecological dynamics. 

Further, these patterns in discharge provide a 

useful context for considering the annual and 

seasonal patterns observed in UMRS water 

quality.

Table 2.2. Mean and standard deviation (SD) for discharge (cfs) from the 9-year sampling period for each study reach by 

season.

Study

reach

Winter

(December–February)

Spring

(March–May)

Summer 

(June–August)

Fall 

(September–November)

Mean SD Mean SD Mean SD Mean SD

Pool 4 12,215 1,815 42,919 14,845 30,161 14,971 16,520 6,016

Pool 8 21,791 4,395 63,154 18,875 45,590 19,503 27,649 8,483

Pool 13 38,019 3,832 95,314 22,218 74,599 29,434 45,032 12,660

Pool 26 88,240 22,903 203,659 59,715 174,322 80,604 88,268 50,039

Open River 177,119 46,876 365,809 96,970 328,034 136,060 184,121 98,108

La Grange Pool 16,122 6,728 24,521 8,442 18,787 8,060 10,179 7,165
7

Figure 2.2. Standardized seasonal annual mean discharges for the six gages near the Long Term Resource Monitoring 

Program study reaches during the 9-year sampling period (1993–2001). Discharge data were standardized using the 

mean and standard deviations by season for each study reach for the 9-year period, where the units on the y-axis are 

standard deviations from the 9-year period mean.
8

Table 2.3. Discharge conditions relative to mean discharge (1993–2001) by season and by study reach for the 9-year study periodvery high (H), high (H), low (L), or very low (L) based on standard deviation (SD) from the mean, with very high and very low beinand high and low being between 0.5 and 1 SD from the mean. Column heading is a numerical code where 1 = Pool 4; 2 = Pool 8; 3= Open River; and 6 = La Grange Pool.

Year

Winter Spring Summer 

1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 

1993 L H H H H H H H H H H H H H H 1994 H H H L L L L L L L H 1995 L H 1996 H H L L L L L L H 1997 H H H H H H L L L L 1998 L L H H H L L L 1999 H H L 2000 L L L L L L L L L L L L L L L L 2001 L L L L H H H H L L L 
9

Figure 2.3. Standardized seasonal annual mean discharges for the six gages near the Long Term Resource Monitoring 

Program study reaches during the 9-year sampling period (1993–2001). Discharge data were standardized using the mean 

and standard deviations by season for each study reach for a 60-year period (1942–2001), where the units on the y-axis are 

standard deviations from the 60-year mean.
10

Figure 2.4. Yearly seasonal mean discharge (cfs) at Clinton, Iowa, for a 128-year period (1874–2001). The fitted line represents a 

third-order polynomial relation.
11

Chapter 3: Spatial Patterns in Suspended Solids, Turbidity, and Chlorophyll a

by

Robert M. Burdis

Background

Anthropogenic activity in the United States 

has altered land use and land cover causing 

increased runoff and erosion of susceptible 

land. This is particularly evident in streams 

and rivers in areas of intense agriculture where 

farming activities on floodplains and in riparian 

zones have been identified as principal sources 

of sediment (Waters 1995). Agriculture, which 

accounts for more than 60% of the land use in the 

Upper Mississippi River Basin (Gowda 1999), 

has greatly affected water quality in the Upper 

Mississippi River System (UMRS). In some areas 

of the UMRS, biological assemblages have been 

altered because of the increase of sediment and 

nutrients into the system. For example, benthic 

algal communities, common in Lake Pepin in 

presettlement times, have been greatly reduced 

because of shading by increased turbidity 

from suspended sediments and phytoplankton 

(Engstrom and Almendinger 2000).

Suspended solids, turbidity, and chlorophyll 

a are common measures of water quality that 

reflect the amount of various materials in the 

water column. Total suspended solids (TSS) is all 

the material suspended in the water, both biotic 

and abiotic, that can be removed by filtration. 

Total suspended solids is composed of organic 

(volatile) and inorganic fractions. Phytoplankton, 

bacteria, and nonliving organic material in the 

water column comprise the volatile suspended 

solids. Chlorophyll a is an indicator of the 

abundance of phytoplankton biomass in the 

water column. Turbidity is a measure of the 

light scattering properties of water. As turbidity 

increases, light is attenuated more rapidly with 

depth because of scattering and absorption. 

Many contaminants in the UMRS are 

associated with suspended particles and, 

thus, the transport and biological availability 

of contaminants are tied to the movement of 

suspended material in the system (Wiener et al. 

1984). The negative effects on aquatic organisms 

produced by the deposition of suspended material 

and the degradation of habitat have been well 

documented (Waters 1995). Total suspended 

solids strongly affects the depth of light 

penetration, which can affect the distribution 

and abundance of macrophytes (Korschgen et al. 

1997).

Methods

The analyses in this chapter focused on 

suspended solids, turbidity, and chlorophyll a

in contiguous backwaters (hereafter referred 

to as backwaters) and the main channel. These 

areas were chosen because they represent an 

informative contrast in both depth and current 

velocity. The main channel areas are deep and 

have high current velocity, backwaters are 

generally shallow and have low current velocity. 

Other common types of aquatic areas in the river 

include side channels and impoundments that are 

generally intermediate in both depth and current 

velocity. Surface water samples collected during 

stratified random sampling (SRS) episodes from 

1993 to 2001 were analyzed for spatial and 

seasonal patterns. In the Upper Mississippi River 

(UMR), Pool 4 is unique because it contains 

Lake Pepin, a natural 10,300-ha lake created by 

the Chippewa River delta. For analysis, Pool 4 

was partitioned into an upper reach (above 

Lake Pepin) and a lower reach (below Lake 

Pepin) because of the marked effects Lake Pepin 

has on suspended solids and turbidity.

Results

Longitudinal Patterns in Summer Concentrations 

of Suspended Solids and Chlorophyll a

There were strong longitudinal patterns 

in summer TSS concentrations among the 

study reaches. Summer TSS concentrations in 
12

upper Pool 4 are high compared to the other 

two northern study reaches (Pools 8 and 13; 

Figure 3.1A). Most of this suspended material 

is inorganic sediment that originates in the 

agriculture-dominated Minnesota River Basin 

(Nielsen et al. 1984; James et al. 2000). The 

Minnesota River has a large influence on water 

quality in the upper reach of the UMR because 

it not only carries a large amount of suspended 

material, but it also contributes about 40% of the 

discharge at the confluence with the Mississippi 

River.

As the Mississippi River enters Lake Pepin, 

it becomes more lacustrine because of the 

change in morphometry. This results in the 

settling of suspended material in Lake Pepin 

where about 85% of the inorganic suspended 

solids are retained. Mean total suspended solids 

concentrations on the entire UMR are lowest 

just below Lake Pepin and increase downstream 

in each of the study reaches from lower Pool 4 

to Open River (Figure 3.1A). Pool 26 is the 

first of the downstream study reaches to exhibit 

TSS concentrations similar to upper Pool 4. 

Tributaries in the southern reaches of the system 

drain agricultural areas that can contribute high 

concentrations of suspended material (Soballe 

and Wiener 1999; Wasley 2000). In contrast, 

tributaries draining forested regions, typical in 

the upper portions of the UMRS (e.g., Chippewa, 

Black, and Wisconsin Rivers), have lower 

suspended solids concentrations and may cause 

a dilution effect. The increase in TSS in study 

reaches from lower Pool 4 to Open River is 

probably because of the cumulative impacts of 

tributary inputs (Chapter 6). The Illinois River 

Basin is also dominated by agriculture. Total 

suspended solids concentrations in La Grange 

Pool of the Illinois River are similar to those of 

Pool 26 and the Open River of the Mississippi 

River. 

Summer TSS concentrations are typically 

higher in the backwaters than in the main 

channel (Figure 3.1A), with the exception of 

Pool 13 and La Grange Pool where main channel 

solids concentrations are slightly higher. The 

higher concentrations in backwaters may be 

due in part to greater phytoplankton abundance 

(measured as chlorophyll a; Figure 3.1E) and 

sediment resuspension. Backwaters typically 

have relatively shallow water depths that makes 

them subject to sediment resuspension because 

of wind and wave action. Bottom-feeding fish 

(e.g., common carp Cyprinus carpio) have been 

implicated as the main cause of turbidity in 

shallow lakes (Scheffer et al. 1993) and may be 

contributing to resuspension of sediments in the 

backwaters of the UMR. Johnson (1994) reported 

an increase in turbidity in the littoral zone of the 

main channel in upper Pool 4 associated with an 

increase in recreational boating activity.

Phytoplankton biomass (measured as 

chlorophyll a) is usually greater in backwaters 

than in the main channel (Figure 3.1E). The 

higher phytoplankton abundance in backwaters 

results in organic material (volatile suspended 

solids) comprising a larger fraction of TSS in 

the backwaters relative to the main channel 

(Figure 3.1C). An exception to this occurs in 

lower Pool 4 where the proportion of volatile 

suspended solids in the main channel is slightly 

higher. This is the result of Lake Pepin being 

both a source of algae and a trap for inorganic 

material. 

In the study reaches downstream from lower 

Pool 4, the proportion of volatile suspended 

solids decreases (Figure 3.1C), even though 

summer chlorophyll a concentrations are 

similar in lower Pool 4, Pools 8 and 13, and 

increase in Pool 26 and La Grange Pool 

(Figure 3.1E). This pattern reflects that inorganic 

suspended solids increase downstream at a 

greater rate than volatile suspended solids 

(Figures 3.1B and 3.1D). The three Long Term 

Resource Monitoring Program (LTRMP) study 

reaches with the highest mean chlorophyll a

concentrations in the backwaters (i.e., upper 

Pool 4, Pool 26, and La Grange Pool) also have 

the highest proportion of inorganic suspended 

solids (Figures 3.1C and 3.1E). These high 

chlorophyll a concentrations may be because 

of the longer residence time of water in some 

backwaters, which allows phytoplankton 

biomass to accumulate despite the high inorganic 

suspended solids concentrations that can 

inhibit phytoplankton growth by reducing light 

penetration. 
13

Figure 3.1. (A) Mean total suspended solids (mg/L), (B) volatile suspended solids (mg/L), (C) percent volatile suspended 

solids, (D) inorganic suspended solids (mg/L), and (E) chlorophyll a (μg/L) in the main channel and backwaters in the Long 

Term Resource Monitoring Program (LTRMP) study reaches during summer stratified random sampling. Means include all 

years from 1993 through 2001. Error bars represent +/- one standard deviation.
14

Longitudinal and Seasonal Patterns in Turbidity 

and Chlorophyll a

Seasonal and spatial differences in turbidity 

exist among the backwaters and main channels 

of the LTRMP study reaches (Figure 3.2). 

Because turbidity is largely determined by TSS, 

the variation among study reaches in turbidity 

was similar to that of TSS. There was a marked 

decrease in turbidity between upper and lower 

Pool 4; lower Pools 4 and 8 were similar; and 

turbidity increased in Pools 13 and 26. These 

longitudinal patterns are similar for the main 

channel and backwaters, although turbidity is 

generally higher in backwaters (Figure 3.2). 

In the main channel, distinct winter minima 

in turbidity were observed in the northern three 

study reaches (Pools 4, 8, and 13; Figure 3.2A). 

This is most likely caused by the minimal runoff 

and ice and snow cover in winter. The ice and 

snow cover reduces light availability for algal 

production and eliminate sediment resuspension 

by wind and waves. Winter turbidity minima 

were not as distinct in the main channel of 

Pool 26 and Open River where ice cover is 

uncommon. Minimum median turbidity for 

the main channel of Pool 26 and Open River 

occurred in winter, but unlike the northern three 

study reaches, the variability in winter turbidity 

remained high, and the difference between winter 

and the other seasons was not as distinct. In the 

main channel of La Grange Pool, which also 

experiences less ice cover than the northern three 

study reaches, similar turbidity is observed in all 

seasons. In Pool 26 and Open River, maximum 

main channel turbidity occurred in spring. 

In backwaters, distinct winter minima were 

observed in all six study reaches (Figure 3.2B). 

This contrasts with the main channel turbidity 

that only exhibited distinct winter minima in the 

northern three study reaches. Thus, for Pool 26, 

Open River, and La Grange Pool, the winter 

minima were more pronounced, and variability 

was lower in the backwaters than in the main 

channel. Highest turbidity was observed in 

summer in all six study reaches. In upper Pool 4 

backwaters, fall turbidity was similar to summer 

and notably higher than winter and spring. 

The high turbidity in summer may be caused 

by high algal biomass, wind-driven sediment 

resuspension, or fish activity.

Chlorophyll a exhibits a distinct winter 

minimum in the main channel and backwaters 

of all study reaches (Figure 3.3B). Fewer 

hours of daylight, lower temperatures, and the 

reduction of light intensity in the water column 

because of ice and snow cover (particularly in 

the upper study reaches), may contribute to this 

pattern. Median main channel chlorophyll a

concentration is highest for Pools 4, 8, and 13 

in spring (Figure 3.3A); for the remaining study 

reaches (Pool 26, Open River, and La Grange 

Pool), median chlorophyll a concentration is 

generally lower in spring than summer and fall, 

perhaps because of reduced light penetration 

caused by high turbidity (Figure 3.2). The main 

channel of Pool 26 is an exception to this pattern 

and has lower chlorophyll a concentrations in fall 

than in spring. In Pools 4, 8, and 13, backwater 

chlorophyll a concentration spans a similar 

range in summer, fall, and winter, but in Pool 26 

and La Grange Pool there is a distinct summer 

maximum in chlorophyll a concentrations 

(Figure 3.3B). 

Habitat and Management Implications

Suspended material in aquatic systems is a 

natural and important part of the ecosystem. 

Algae, for example, are an important source of 

food in the aquatic food web. However, excessive 

amounts of suspended material, whether organic 

or inorganic, can have deleterious effects on 

the biota of an aquatic system. Several studies 

have documented the negative effects of 

turbidity on prey capture by fishes (Gardner 

1981; Vandenbyllaardt et al. 1991; Reid et al. 

1999). Miner and Stein (1996) documented 

turbidity affecting the selection of habitat use 

by fish. Turbidity can affect the growth and 

productivity of aquatic macrophytes (Kimber 

et al. 1995; Korchgen et al. 1997; Doyle and 

Smart 2001) by reducing light penetration and 

may have contributed to a decline in submersed 

macrophytes on parts of the UMRS in the early 

1990s (Rogers 1994). In shallow lakes, turbidity 

levels can determine whether a system is in a 
15

Figure 3.2. Box plots of winter, spring, summer, and fall turbidity (in nephelometric turbidity units [NTU]) in (A) main channel 

and (B) backwaters in the Long Term Resource Monitoring Program study reaches during stratified random sampling from 

1993 through 2001. Box plots represent the 10th, 25th, 50th, 75th, and 90th percentiles.
16

Figure 3.3. Box plots of winter, spring, summer and fall chlorophyll a concentrations (μg/L) in (A) main channel and 

(B) backwaters in the Long Term Resource Monitoring Program study reaches during stratified random sampling 

from 1993 through 2001. Box plots represent the 10th, 25th, 50th, 75th, and 90th percentiles.
17

clear state dominated by aquatic macrophytes 

or in a turbid state characterized by high algal 

biomass (Scheffer 1993). Suspended sediments 

can also negatively affect filter-feeding 

organisms, such as zooplankton (Arruda et al. 

1983) and mussels (Aldridge et al. 1987). 

The LTRMP data show that turbidity and 

suspended solids concentrations in the UMRS 

(Figures 3.1 and 3.2) are sometimes at levels 

that negatively affect aquatic organisms. Gardner 

(1981) found feeding rates for bluegills Lepomis 

macrochirus were reduced at 60 nephelometric 

turbidity units (NTU) and above; Reid et al. 

(1999) found lower rates of prey capture for 

largemouth bass Micropterus salmoides at 

70 NTU; and Vandenbyllaardt et al. (1991) 

found walleye Stizostedion vitreum feeding was 

inhibited at 100 NTU. Doyle and Smart (2001) 

found that average turbidities of approximately 

40 NTU decreased growth and survival of wild 

celery Vallisneria americana winterbuds and 

seedlings. Arruda et al. (1983) found suspended 

sediment concentrations of 50 to 100 mg/L 

reduced the amount of algal carbon ingested 

by Daphnia to potential starvation levels. The 

LTRMP data indicate these levels of suspended 

solids concentrations and turbidity are common 

in some parts of the UMRS. The mean TSS 

concentrations in upper Pool 4, Pool 26, Open 

River, and La Grange Pool (Figure 2.1A) indicate 

that these study reaches are chronically turbid. 

Although the turbidity and concentration of 

suspended solids are at levels to affect biota, the 

duration that these levels persist may be just as 

important. Newcombe and MacDonald (1991) 

reviewed more than 70 articles on the effects 

of inorganic suspended sediments on fish and 

invertebrates and found that suspended sediment 

concentration alone was a poor predictor of 

effects, but that concentration along with duration 

was a much better indicator. The timing of 

high turbidity events may also be significant to 

the growth and survival of organisms. Aquatic 

organisms may be exceptionally vulnerable to 

high turbidity during certain life-history stages. A 

high turbidity event in late fall, for example, may 

not have the same effect as an event in spring 

or summer when many organisms are in early 

life-history stages and when peak growth of most 

organisms occurs.

The discharge regime over the period of 

record was above average with no extended 

periods of low flow (Chapter 2). In general, 

inorganic material was the main source of 

turbidity, particularly in the more turbid reaches 

of the system. Under low discharge conditions, 

suspended solids consist of a higher proportion of 

volatile suspended solids because of an increase 

in algal biomass and a reduction of inorganic 

sediment load into the system. Many studies 

have shown the importance of discharge and 

water residence time in controlling algal biomass 

(Baker and Baker 1979; Soballe and Kimmel 

1987; Heiskary and Markus 2001). As discharge 

decreases, water residence time increases, which 

allows algal biomass to accumulate. In the 

UMRS, significant negative correlations exist 

between discharge and chlorophyll a in the main 

channel area of upper Pool 4, Pools 8 and 13, and 

La Grange Pool and in the backwaters of upper 

Pool 4, Pool 8, and La Grange Pool (Figure 3.4).

 Scheffer et al. (1993) suggested shallow lakes 

can have two alternative stable states: a clear 

state dominated by aquatic macrophytes and a 

turbid state characterized by high algal biomass. 

Although many mechanisms are probably 

involved, Scheffer et al. (1993) hypothesized that 

shallow lake systems are driven primarily by the 

interaction between submersed vegetation and 

turbidity. The mechanisms include macrophyte 

enhancement of water clarity and the inhibition 

of vegetation growth because of turbidityinduced light limitation. The LTRMP data 

suggest a turbidity threshold may have been 

reached for aquatic macrophytes in upper Pool 4, 

Pool 26, and La Grange Pool on the basis of high 

turbidities, high chlorophyll a concentrations, 

and a lack of submerged aquatic macrophytes 

in these study reaches (Rogers and Theiling 

1999; Upper Mississippi River Conservation 

Committee 2003). Aquatic macrophytes 

declined rapidly in the late 1950s on the Illinois 

River (Sparks 1984) in large part because of 

an increased sediment load. Upper Pool 4 and 

upper Lake Pepin, which are presently turbid 

and nearly devoid of vegetation, had extensive 

macrophyte beds until the 1960s (Jack Enblom, 

Minnesota Department of Natural Resources, 

personal communication) indicating that the 
18

Figure 3.4. Correlation between mean discharge (cfs) and mean chlorophyll a (μg/L) in the main channel and 

backwaters in the Long Term Resource Monitoring Program study reaches ([A] upper Pool 4, [B] lower Pool 4, 

[C] Pool 8, [D] Pool 13, [E] Pool 26, [F] Open River, and [G] La Grange Pool) during summer stratified random sampling 

(1993–2001). No data are available from 1993 for Pool 26 and Open River. Open River has no backwater stratum. 
19

system received perturbations creating conditions 

no longer conducive to the growth of submersed 

macrophytes. This points to the important role 

Lake Pepin plays in the UMRS and suggests 

that study reaches below Lake Pepin would be 

more turbid and have less vegetation without the 

extensive settling of sediment in the lake. 
20

Chapter 4: Seasonal and Annual Variation in Nitrogen, Phosphorous, and Chlorophyll a

by

Lori A. Soeken-Gittinger and Jeffrey N. Houser

Background

Nitrogen and phosphorous are both critical 

plant nutrients and play an essential role in 

biochemical reactions and biological metabolism. 

The waters of the Upper Mississippi River 

System (UMRS) are eutrophic and nitrogen 

and phosphorous typically do not limit primary 

production (Patrick 1988), but these nutrients 

may be limiting at certain times and places. 

Chlorophyll a is an indicator of phytoplankton 

biomass and is one component of primary 

production in the UMRS. Phytoplankton is a food 

source for many organisms in the river, including 

mussels, invertebrates, and fish.The seasonal and 

annual cycles of nutrients and chlorophyll a can 

affect the biota of the river floodplain ecosystems 

including aquatic plants, macroinvertebrates, 

and fish. Understanding nutrient sources, 

transport, storage, cycling, and losses in the 

UMRS is essential to system management and 

maintenance. 

Nutrients and chlorophyll a concentrations 

vary temporally (seasonally and annually) 

and spatially. Annual variations in nutrient 

concentrations are more pronounced in streams 

and rivers than in lakes (Horne and Goldman 

1994). The causes of this variation are not 

well understood, and many factors influence 

year-to-year fluctuations such as climate, 

flood timing and duration, anthropogenic 

disturbance, and internal loading. A peak in 

nutrient concentrations is expected during the 

spring flood because of increased inputs from 

the floodplain and watershed, but might also 

occur in certain locations during periods of low 

flow if point source effluents do not decline in 

conjunction with declining water levels (Sparks 

1984) or because of internal loading from the 

sediments. 

The objectives of this chapter were to 

examine the seasonal and annual fluctuations of 

nutrients and chlorophyll a within the UMRS 

in main channel and contiguous backwater 

areas (hereafter referred to as backwaters). We 

focused on three nutrient and primary production 

constituents: soluble reactive phosphorous, 

nitrate + nitrite nitrogen, and chlorophyll a

(Horne and Goldman 1994). Soluble reactive 

phosphorous (SRP) approximates the amount of 

phosphorous available for use by phytoplankton, 

bacteria, algae, and aquatic macrophytes 

(Lampert and Sommer 1997). Total oxidized 

nitrogen is the sum of nitrate and nitrite nitrogen 

(American Public Health Association 1992), 

referred to in this chapter as nitrate + nitrite 

nitrogen (NOx). Nitrate is the most highly 

oxidized form of nitrogen and usually the most 

abundant form of inorganic nitrogen in aquatic 

systems, whereas nitrite is usually present only in 

small amounts (Horne and Goldman 1994). 

Methods

The analyses in this chapter focus on NOx, 

SRP, and chlorophyll a in the main channel 

and backwaters sampled during fixed-site and 

stratified random sampling (SRS) periods 

(Chapter 1). Only surface samples (about 20 cm 

below surface) were included in the analyses. 

Field and laboratory methods are described in 

Soballe and Fischer (2004).

Means and standard error were calculated 

in SAS (version 8.02). Fixed-site means were 

calculated by month, and SRS means were 

calculated by seasonal episode. The SRS data 

were collected from 1993 to 2002. However, SRS 

sampling did not begin until summer 1993, so 

there are no SRS data for spring 1993. Fixed-site 

data included in this chapter span from 1993 to 

2002.
21

Results and Discussion

Annual Patterns

Patterns in nutrient concentrations in spring 

and summer are of particular interest for the 

UMRS. Highest flows generally occur in spring 

(Figure 2.1) resulting in high rates of nutrient 

export. Summer represents the growing season 

when the interactions of nutrient concentrations 

are most important. In the main channel and 

backwaters of the Upper Mississippi and Illinois 

Rivers, spring SRP concentrations were similar 

among all study reaches (Figure 4.1), suggesting 

that differences in local climate and land use 

had minimal effects on dissolved phosphorous 

concentrations in spring. La Grange Pool showed 

much higher SRP concentration in 1996 than in 

any other years or study reaches; the cause of 

high SRP concentrations in this year is unknown. 

Spring NOx concentrations in the main 

channel and backwaters of the Mississippi 

River showed a strong covariance among study 

reaches (Figure 4.1) probably driven by annual 

differences in discharge. Years of low spring 

NOx concentrations were years of relatively low 

discharge (Chapter 2). Nitrate concentrations in 

streams and rivers have been related to rainfall, 

with nitrogen increasing in proportion to 

discharge (Horne and Goldman 1994). Reduced 

precipitation can result in less export of nitrogen 

from the surrounding agricultural land into the 

river.

La Grange Pool of the Illinois River 

consistently showed substantially higher NOx

concentrations when compared to Mississippi 

River study reaches. High inputs of nitrogen to 

the Illinois River were not surprising because 

the Illinois River flows through the portion of 

the UMRS watershed with the highest estimated 

nitrogen fertilizer use (Gowda 1999). In addition, 

the Illinois River had a much lower discharge 

than the Mississippi River, which resulted in less 

dilution of these terrestrial NOx inputs.

Spring means of chlorophyll a did not exhibit 

the strong covariance among Long Term 

Resource Monitoring Program study reaches 

that was seen for NOx (Figure 4.1). This lack 

of covariance suggests local factors, such as 

aquatic vegetation abundance, climate, watershed 

conditions, or local nutrient inputs affected 

year-to-year variation and systemic patterns 

in chlorophyll a. In spring 2000, most study 

reaches exhibited similar and high chlorophyll 

a concentrations. This was probably because of 

low discharge throughout the system that spring 

(Figure 2.2) that increased hydraulic retention 

time and reduced turbidity from inorganic 

suspended solids.

Summer nutrient concentrations were lower 

than spring concentrations, particularly for NOx

(Figure 4.2). In contrast, maximum chlorophyll 

a concentrations were higher in summer than 

in spring, particularly for the backwaters of 

La Grange Pool of the Illinois River and Pool 26.

Summer SRP concentrations in the main 

channel of the Upper Mississippi River were 

similar among all study reaches, but, as was 

seen for NOx concentrations, the main channel 

of La Grange Pool (Illinois River) exhibited 

higher concentrations of SRP than any of the 

Mississippi River study reaches (Figure 4.2). In 

some years (1997, 1999, 2001), summer SRP 

concentrations in backwaters were significantly 

greater in Pool 13 and La Grange Pool than 

in other study reaches (Figure 4.2). The cause 

of this high variation is unknown, but these 

differences did not appear to correspond to high 

or low discharge (Chapter 2). 

Summer NOx in the Illinois and Mississippi 

Rivers showed no clear differences among study 

reaches in the main channel and backwaters 

(Figure 4.2). The NOx concentration was 

generally lower in the backwaters than in the 

main channel. This is probably because of higher 

rates of denitrification (Richardson et al. 2004) 

and primary production in the backwaters and 

limited delivery of NOx to backwaters during low 

summer flows.

Summer chlorophyll a concentrations in the 

main channel of Pool 8 and the Illinois River 

were significantly higher in certain years than 

in other study reaches. The Illinois River also 

had higher concentrations of SRP than other 

study reaches, and this nutrient availability 

may have contributed to higher chlorophyll 

a concentrations. The reasons for higher 
22

Figure 4.1. Annual means of soluble reactive phosphorous (mg/L), nitrate + nitrite oxygen (mg/L; NOx), and chlorophyll 

a (μg/L) in the main channel and backwaters of the Upper Mississippi and Illinois Rivers based on spring stratified 

random sampling (SRS) from 1994 to 2002. Error bars represent +/- one standard error.

chlorophyll a in Pool 8 are unknown. Backwaters 

of the Illinois River and Pool 26 exhibited much 

higher summer chlorophyll a concentrations 

compared to other study reaches (Figure 4.2). 

This may be because the backwaters of these 

two study reaches had little aquatic vegetation 

to compete with phytoplankton for nutrients. 

These backwaters were also relatively shallow, 
23

Figure 4.2. Annual means of soluble reactive phosphorous (mg/L), nitrate + nitrite nitrogen (mg/L; NOx), and chlorophyll 

a (μg/L) in the main channel and backwaters of the Upper Mississippi and Illinois Rivers based on summer stratified 

random sampling (SRS) from 1993 to 2002. Error bars represent +/- one standard error.

allowing for frequent resuspension of sediment 

and nutrients. The suspended sediments reduce 

the depth of light penetration, making it more 

difficult for aquatic vegetation to become 

established, and the resuspended nutrients 

promote algal production.

Spring and summer SRS data clearly showed 

differences among the Illinois River and the 
24

Mississippi River study reaches. In spring 

of most years, both backwaters and the main 

channel of the Illinois River had higher NOx and 

SRP concentrations (Figure 4.1), and in summer 

the main channel of the Illinois River exhibited 

noticeably higher SRP concentrations than 

Mississippi River study reaches (Figure 4.2). In 

most years, the backwaters of the Illinois River 

had higher summer chlorophyll a concentrations 

than all of the Mississippi study reaches except 

for Pool 26 (Figure 4.2). The Illinois River flows 

into the Mississippi River at Pool 26, and in 

spring and summer the main channel in Pool 26 

often had the highest NOx concentrations of the 

Mississippi River study reaches. The relative 

contributions of nutrients and chlorophyll a from 

the Illinois River and from the many agriculturedominated catchments that enter the river 

between Pools 13 and 26 to the high chlorophyll 

a concentrations in Pool 26 remain unclear. 

The UMR Basin accounts for 31% of the total 

nitrogen delivered from the Mississippi River 

to the Gulf of Mexico (Alexander et al. 1995) 

and, as stated previously, the Illinois River flows 

through the portion of the UMR Basin with the 

highest estimated nitrogen fertilizer use (Gowda 

1999). The Mississippi River has a greater 

discharge and dilution capacity than the Illinois 

River (Sparks 1984); thus, higher fertilizer 

use combined with less dilution most likely 

accounted for the higher NOx concentrations in 

the Illinois River in spring. It is also probable 

that the high NOx concentrations in the Illinois 

River were influenced by loadings from sewage 

treatment plants in Chicago, Illinois; the 

Upper Illinois River exhibited high ammonia 

concentrations that declined downstream as the 

ammonia was converted to nitrate (Sparks 1984). 

Fertilizer use, along with industrial and domestic 

wastes, may also have accounted for higher SRP 

concentrations in summer as well (Starrett 1972).

Seasonal Patterns

Soluble reactive phosphorous concentrations 

in the main channel of the Upper Mississippi 

and Illinois Rivers tended to peak in September 

and exhibited minimum concentrations in April 

and May (Figure 4.3). This is contrary to the 

conventional idea that nutrient concentrations 

in large rivers often peak in late spring or early 

summer in conjunction with spring flooding 

(Horne and Goldman 1994). This trend was 

also seen in backwaters with large SRP 

peaks in summer or early fall and minimum 

concentrations in April and May (Figure 4.3). 

Seasonal NOx concentrations in the main 

channel and backwaters indicated a pattern 

nearly opposite of that shown by seasonal SRP 

patterns, with the lowest concentrations of NOx

in fall, when SRP concentrations are at their 

highest (Figure 4.4). As the lows in nitrogen 

occurred directly following peaks in chlorophyll 

a (Figures 4.4–4.5), it was possible that the 

NOx concentrations were reduced by algal 

assimilation and aquatic macrophytes. High 

rates of denitrification in summer, particularly in 

backwaters (Richardson et al. 2004), probably 

also contributed to the low NOx concentrations 

observed in late summer. A similar seasonal 

distribution of nitrogen was found in many 

eutrophic temperate lakes, where the fall NOx 

minima increase to maxima in late winter 

through summer (Wetzel 1983). This raises 

the possibility that nitrogen was limiting algal 

growth in late summer, especially during low 

flow periods, possibly explaining the higher SRP 

concentrations found during this time.

Chlorophyll a concentrations in main channel 

and backwaters showed peaks in late summer 

and fall, with minima in winter and early 

summer (Figure 4.5). The one exception was the 

backwaters of La Grange Pool where chlorophyll 

a concentrations remained elevated from April 

through September (Figure 4.5). These peak 

chlorophyll a concentrations in early spring and 

or late summer, along with the minima in SRP 

in this same period (Figure 4.3), suggest that the 

low SRP concentrations may have been because 

of algal uptake of SRP.

The fixed-site and SRS data generally show 

good agreement and similar annual patterns. 

There are several notable exceptions. The most 

consistent difference is seen in Pool 26 where 

nutrient and chlorophyll a concentrations 

measured at fixed sites are generally substantially 

lower than the SRS means. In Pool 13 

backwaters, NOx concentration measured at 
25

Figure 4.3. Monthly mean (1993–2001) soluble reactive phosphorous (mg/L) concentrations in the main channel and 

backwaters of the Upper Mississippi and Illinois Rivers. Monthly data are from fixed-site sampling. Stratified random 

sampling (SRS) points are plotted quarterly between the 2 months that the 2-week SRS episode spans. Error bars represent 

+/- one standard error.

the fixed sites is generally lower than the SRS 

mean, particularly in winter. In La Grange 

Pool backwaters, the fixed-site fall mean NOx

concentration is lower than the SRS mean. In 

Pool 8 backwaters, fixed-site fall chlorophyll a

concentrations are higher than the fall SRS mean.

The fixed-site and SRS regimes were designed 

for different purposes. The SRS design provides 

unbiased estimates for each study reach and 

strata, but is limited in its temporal coverage. The 

fixed-site data provide information at a higher 

temporal resolution, which illustrates seasonal 

patterns in nutrients and chlorophyll a. Because 

of the limited spatial extent of the fixed-site 

sampling and subjective-site selection, these data 

do not provide unbiased means for study reaches 

or strata. 

Conclusions

The seasonal and annual patterns addressed in 

this chapter were similar among study reaches 

for some parameters. There were notable 

differences in nutrients in Pool 26 and La Grange 

Pool, and in chlorophyll a in Pools 8 and 26 

and La Grange Pool. Spring NOx concentrations 

were highly variable among years in both the 

main channel and backwaters, but these annual 

differences were similar among study reaches. 

These variations were probably attributable to 
26

Figure 4.4. Monthly mean (1993–2001) nitrate + nitrite (mg/L; NOx) concentrations in the main channel and backwaters of the 

Upper Mississippi and Illinois Rivers. Monthly data are from fixed-site sampling. Stratified random sampling (SRS) points are 

plotted as in Figure 4.3. Error bars represent +/- one standard error.

differences in rainfall and river discharge among 

years. 

There was a substantial difference in 

nutrient and chlorophyll a concentrations in 

La Grange Pool of the Illinois River compared 

to study reaches of the Mississippi River in 

spring and summer. These differences were 

possibly related to the watershed and land-use 

differences, particularly the high use of nitrogen 

fertilizer in the Illinois River Basin. There 

were also differences in the hydrologic regimes 

(particularly residence time) of the Illinois and 

Mississippi Rivers (and among study reaches 

within the Mississippi River). Further analysis of 

the effects of hydraulic residence time on nutrient 

concentrations would be worthwhile.

Contrasting seasonal patterns in nitrogen 

and phosphorous were observed. Evidence 

suggested that algal production was not limited 

by SRP in summer, particularly in June and at 

the end of summer in August and September. 

High concentrations of SRP in association with 

low concentrations of NOx and chlorophyll a in 

summer suggest algal growth may have been 

limited by something other than SRP (e.g., NOx, 

light, etc.) during these times. 

A number of additional analyses would be 

useful in understanding chlorophyll a (and 

therefore phytoplankton) dynamics. Questions 

that remain include the following: Is there a 

consistent relationship between nutrient and 

chlorophyll a concentrations? Is this relationship 

different in the main channel and backwaters 

or among study reaches? What is the role of 

resuspension of sediments in determining 

chlorophyll a concentrations? The resulting 
27

Figure 4.5. Monthly mean (1993–2001) chlorophyll a concentrations (μg/L) in the main channel and backwaters of the Upper 

as in Figure 4.3. Error bars represent +/- one standard error.

increased turbidity will reduce light availability 

(potential negative effect on chlorophyll a), but 

the resuspension may increase nutrient inputs 

to the water column (potential positive effect on 

chlorophyll a). Studies designed to specifically 

address such questions combined with additional 

analysis of the Long Term Resource Monitoring 

Program data will improve our understanding of 

chlorophyll a and nutrient dynamics and increase 

our ability to effectively manage the UMRS.

Month
28

Chapter 5: Spatial and Temporal Variation of Dissolved Oxygen

by

James R. Fischer, Jeffrey N. Houser, Kraig L. Hoff, and Erik Harms

Background

Dissolved oxygen (DO) is an important factor 

in determining habitat suitability and can affect 

physicochemical processes within the water 

column and underlying sediments. The DO 

concentrations in the Upper Mississippi River 

(UMR) are affected by temperature, current 

velocity, and biological processes that produce 

oxygen through photosynthesis and consume 

oxygen through respiration. Variations in these 

factors can produce large spatial and temporal 

variation in DO concentrations. Because low DO 

concentration is a critical factor in determining 

habitat suitability for fish and invertebrates, most 

states along the river recognize a criterion of 

5 mg/L DO as the concentration necessary to 

protect fish and other aquatic organisms (e.g., 

Wisconsin Administrative Code Department of 

Natural Resources Chapter NR 102 [1998]).

Municipal sewage disposal has historically 

been an important point source of oxygendemanding materials to the UMR and a major 

contributor to oxygen depletion in many parts 

of the river (Wiebe 1927; Fremling 1964). 

Before changes made in response to the Clean 

Water Act (1977), oxygen concentrations in 

some parts of the river were low enough that 

sensitive invertebrate species (e.g., mayflies such 

as Hexagenia spp.) disappeared. Improvement 

in municipal sewage treatment has reduced 

the effect of sewage discharge on the river and 

sensitive species have returned to many areas 

where they were historically present (Fremling 

1989). 

In addition to point sources, oxygen demand 

also results from nonpoint terrestrial and aquatic 

sources. The Minnesota River, for example, is a 

major source of organic matter to Pool 2 on the 

UMR. Microbial decomposition of such organic 

matter is an important source of oxygen demand. 

Zebra mussels, Dreissena polymorpha, first 

documented in the system in 1991 (Cope et al. 

1997), may contribute to oxygen demand through 

excretion and respiration at a rate of about 15 

to 20 mg O2 m-2 d-1 (Sullivan and Endris 1998). 

High zebra mussel densities have depleted 

oxygen concentrations in the Seneca River, New 

York (Effler and Siegfried 1994), and in some 

reaches of the UMR. 

An evaluation of DO dynamics in space 

and time is necessary to develop potential 

management strategies for the UMR. This 

chapter provides a broad overview of the oxygen 

dynamics within study reaches of the Long Term 

Resource Monitoring Program (LTRMP) on 

the Upper Mississippi River System (UMRS) 

and illustrates some of the spatial and temporal 

variability of DO in this complex system. This 

initial review establishes a baseline summary 

and identifies areas of interest for additional 

analyses. Specifically this chapter addresses 

(1) differences among river reaches and 

among years, (2) seasonal patterns, and (3) the 

occurrence of low DO concentrations in winter 

and summer. 

Methods

The following variables from LTRMP 

stratified random sampling (SRS) data were 

used in our analysis: surface dissolved oxygen 

concentrations, percent dissolved oxygen 

saturation, and snow and ice thickness. Surface 

(0.2 m) dissolved oxygen was measured in 

situ with a multiparameter sonde (Hydrolab 

Datasonde 3® or Minisonde 4a®; Hach 

Company, Loveland, CO) equipped with a 

polarographic type membrance electrode 

(Soballe and Fischer 2004). A small number 

of data points (<1%) were DO concentrations 

denoted as “off scale high” (Quality factor code 

= 2; Soballe and Fischer 2004), and these data 

points were omitted from the figures presented 

in this chapter. Data from 1993 to 2002 for all 

study reaches and the following strata were 

included unless otherwise specified: contiguous 

backwaters, impoundment, side channel, main 
29

channel, and Lake Pepin (Pool 4) and Swan Lake 

(Pool 26). The SRS sampling began in summer 

1993 for Pools 4, 8, and 13 and La Grange Pool 

and began in fall 1993 for Pool 26 and Open 

River. 

We determined the area of low DO (<5 mg L) 

in contiguous backwater areas (hereafter referred 

to as backwaters) by assuming that surface DO 

measured at each SRS site characterized the grid 

cell it represented and summing the area of all 

grid cells with low DO. Grid cells were 200-m 

squares for all strata in 1993 to 1995. In 1995, 

the grid cells in backwaters and side channels 

were reduced to 50-m squares. For winter, sites 

that were frozen to the bottom were included in 

the total area of low DO because these frozen 

areas were also unsuitable habitat for most 

organisms of interest. 

Results and Discussion

Seasonal Means by Study Reaches

In spring, median DO in Pools 4, 8, and 13 

were higher (10 to 15 mg/L) than in Open River 

(7 to 10 mg/L; Figure 5.1). Concentrations in 

Pool 26 and La Grange Pool were intermediate. 

Virtually, no DO concentration <5 mg/L were 

observed in spring.

In summer, median DO concentrations in 

Open River were lower than in northern reaches 

(Pools 4, 8, and 13), but no obvious differences 

existed among the three northern study reaches 

and Pool 26 (Figure 5.2). Median concentrations 

were between 5 and 10 mg/L across all study 

reaches. All reaches occasionally had low 

summer DO (<5 mg/L). Pools 8 and 13 and 

La Grange Pool showed the highest frequency 

of low summer DO conditions (Figure 5.2) and 

Open River had the fewest occurrences. The 

northern study reaches (Pools 4, 8, and 13) 

have more backwater areas than the southern 

study reaches (Pool 26, La Grange Pool, and 

Open River [which has no backwaters]); and, 

in summer, backwaters were characterized by 

relatively long residence times that facilitate DO 

depletion. It is unknown why Pool 4 experienced 

less frequent low DO conditions than the other 

northern study reaches. 

In fall, DO patterns were similar to 

summer, although the occurrence of low DO 

concentrations was less frequent (Figure 5.3). 

In winter, distinct north–south differences were 

apparent (Figure 5.4). Median DO concentrations 

were generally between 10 and 16 mg/L in all 

study reaches. However, DO concentrations

<5 mg L-1 occurred regularly in the northern three 

study reaches, but rarely occurred in Pool 26 

and La Grange Pool and never occurred in Open 

River. The northern study reaches showed a large 

decrease in median DO concentration between 

1995 and 1996 and a general increase from 1997 

through 2002 (Figure 5.4). 

Summary of Seasonal Patterns

In the northern study reaches, median DO 

concentrations are higher in spring and winter, 

and lower in summer and fall. In the southern 

study reaches, DO concentrations are highest 

in winter, lowest in summer, and intermediate 

in spring and fall. Important drivers of these 

seasonal patterns in DO are water temperature, 

current velocity (a function of discharge), and 

ice and snow cover. The solubility of oxygen 

in water is negatively correlated with water 

temperature. Current velocity determines the 

extent of vertical mixing and turbulence, which 

affects the rate of oxygen exchange with the 

atmosphere, and residence time, which affects 

oxygen depletion rates. Ice prevents gas exchange 

with the atmosphere. However, if the ice is clear, 

high rates of photosynthesis can occur resulting 

in high DO concentrations. If significant snow 

cover reduces light penetration, respiration will 

be the dominant biological process resulting in 

low DO concentrations. The effects of snow and 

ice cover can be clearly seen for the UMR. Total 

snow and ice thickness explain about half of the 

variability among study reaches in mean winter 

backwater DO (Figure 5.5). 

For the northern study reaches, spring is a time 

of low water temperature, high discharge, and 

little ice cover resulting in relatively high DO 

concentrations. In winter, low discharge and 

substantial ice and snow cover, particularly in 

backwaters, result in lower DO concentrations 

relative to spring and low DO concentrations 

occur regularly in backwaters. In summer, low 
30

 Study Reach = Pool 13 (C) Study Reach = Pool 4 (A) Study Reach = Pool 8 (B)

 Study Reach = La Grange Pool (F) Study Reach = Pool 26 (D) Study Reach = Open River (E)

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Figure 5.1. Spring dissolved oxygen (DO) in all strata of the six study reaches based on the Long Term Resource Monitoring Program stratified random sampling data, 1994–2002. Boxes indicate the 25th–75th percentile, the horizontal line within the box represents the median, whiskers extend to the largest and or smallest value within 1.5 × the interquartile range (75th–25th percentile), and points represent observations outside this range. The solid line at DO = 5 mg/L indicates DO concentration generally recognized as necessary to protect most aquatic organisms.
31

 Study Reach = Pool 13 (C) Study Reach = Pool 4 (A) Study Reach = Pool 8 (B)

 Study Reach = Pool 26 (D) Study Reach = Open River (E)

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

 Study Reach = La Grange Pool (F)

Figure 5.2. Summer dissolved oxygen (DO) in all strata of the six study reaches based on the Long Term Resource Monitoring Program stratified random sampling data, 1993–2002. Boxes indicate the 25th–75th percentile, the horizontal line within the box represents the median, whiskers extend to the largest and or smallest value within 1.5 × the interquartile range (75th–25th percentile), and points represent observations outside this range. The solid line at DO = 5 mg/L indicates DO concentration generally recognized as necessary to protect most aquatic organisms.
32

 Study Reach = Pool 13 (C) Study Reach = Pool 4 (A) Study Reach = Pool 8 (B)

 Study Reach = La Grange Pool (F) Study Reach = Pool 26 (D) Study Reach = Open River (E)

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) 

Figure 5.3. Fall dissolved oxygen (DO) in all strata of the six study reaches based on the Long Term Resource Monitoring Program stratified random sampling data, 1993–2002. Boxes indicate the 25th–75th percentile, the horizontal line within the box represents the median, whiskers extend to the largest and or smallest value within 1.5 × the interquartile range (75th–25th percentile), and points represent observations outside this range. The solid line at DO = 5 mg/L indicates DO concentration generally recognized as necessary to protect most aquatic organisms.
33Study Reach = La Grange Pool (F) Study Reach = Open River (E)

 Study Reach = Pool 13 (C) Study Reach = Pool 4 (A) Study Reach = Pool 8 (B)

 Study Reach = Pool 26 (D)

Dissolved Oxygen (mg/L) Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) Dissolved Oxygen (mg/L) 

Dissolved Oxygen (mg/L) Dissolved Oxygen (mg/L) 

Figure 5.4. Winter dissolved oxygen (DO) in all strata of the six study reaches based on the Long Term Resource Monitoring Program stratified random sampling data, 1994–2002. Boxes indicate the 25th–75th percentile, the horizontal line within the box represents the median, whiskers extend to the largest and or smallest value within 1.5 × the interquartile range (75th–25th percentile), and points represent observations outside this range. The solid line at DO = 5 mg/L indicates DO concentration generally recognized as necessary to protect most aquatic organisms.
34

Figure 5.5. Dissolved oxygen (DO) saturation versus average snow and ice depth for the backwaters of the Long Term 

Resource Monitoring study reaches, 1994–2002; Open River has no backwater stratum.

discharge reduces the exchange between the 

main channel and backwaters and side channels. 

The increased residence time and high rates of 

biological respiration in summer often produce 

low DO conditions in backwaters. 

For the southern study reaches (Pool 26, Open 

River, and La Grange Pool), seasonal patterns 

are somewhat different. The DO concentrations 

are highest in winter partly because there is 

little ice and snow cover in these study reaches 

in winter, and water temperatures are cool. 

In spring, DO concentrations are lower in the 

southern study reaches than in the northern 

study reaches, perhaps because of higher water 

temperatures. Like the northern study reaches, 

the DO concentrations are generally lowest in 

summer in the southern study reaches. Fall DO 

concentrations are generally intermediate relative 

to spring and summer concentrations.

Among the study reaches, Open River tends 

to exhibit lower DO concentrations (except 

in winter) and lower variability than the other 

study reaches. These differences may have 

been because of higher temperatures in Open 

River (oxygen solubility decreases with higher 

temperature), or because of higher suspended 

solids (Chapter 3), which can reduce light 

penetration and, therefore, photosynthesis, 

and increase DO demand because of increased 

concentrations of suspended organic material. 

The lower variance in DO in Open River may 

have been because of the reduced habitat 

diversity of this reach relative to the other study 

reaches. There were no backwaters in Open 

River, and backwaters were generally where the 

extremely high and extremely low DO values 

were observed in the other study reaches. 

Spatial Patterns in Low DO Concentrations

The overall occurrence of low, daytime, 

surface DO concentration was infrequent in 

the UMRS (about 4% of the sites monitored 

were <5 mg/L), but low DO was most common 

in summer and winter (Figures 5.2 and 5.4). 

Except in La Grange Pool, backwaters were the 

only strata where low DO concentrations were 

regularly observed (Table 5.1). In winter, low 
35

Table 5.1. Mean proportion of stratified random sampling sites with dissolved oxygen concentration <5 mg/L in winter and 

summer from 1993 to 2001. One standard deviation is shown parenthetically. Bold font indicates where the proportion of 

sites with low dissolved oxygen is >10%.

Study reach

Strata

Main channel Side channel Backwater Lakea Impounded

Winter

 Pool 4 0.004 (0.013) 0.008 (0.02) 0.14 (0.14) 0.007 (0.015) —b

 Pool 8 0 0.005 (0.014) 0.13 (0.09) — 0

 Pool 13 0 0 0.1 (0.05) — 0.004 (0.01)

 Pool 26 0 0.003 (0.008) 0.006 (0.02) 0 0

 Open River 0 0 -- — —

 La Grange Pool 0 0 0.009 (0.03) — —

Summer

 Pool 4 0.008 (0.3) 0.013 (0.03) 0.058 (0.07) 0.003 (0.01)

 Pool 8 0.008 (0.02) 0.013 (0.02) 0.12 (0.08) 0

 Pool 13 0.003 (0.01) 0.023 (0.05) 0.21 (0.14) 0.057 (0.1)

 Pool 26 0.014 (0.04) 0.022 (0.05) 0.13 (0.1) 0.14 (0.2) 0.022 (0.05)

 Open River 0.013 (0.04) 0.032 (0.06)

 La Grange Pool 0.25 (0.24) 0.35 (0.27) 0.067 (0.067)

a

Lake Pepin in Pool 4; Swan Lake in Pool 26.

b

— indicates that stratum was not present in that reach.

DO occurred, on average, in 10% to 14% of 

the backwater sites sampled in Pools 4, 8, and 

13, but did not commonly occur in other study 

reaches or strata (Table 5.1). In summer, the 

backwaters of Pools 8, 13, and 26 exhibit low 

DO concentrations in 12% to 21% of the sites 

sampled (Table 5.1). For La Grange Pool, low 

summer DO is observed regularly in the main 

(25% of sites sampled) and side channel (35% of 

sites sampled) areas.

Areal Extent of Low DO Concentrations

Summer

There was substantial interannual variability 

in the areal extent of low DO conditions in 

backwaters in summer (Figure 5.6). The smallest 

areal extent of low DO was observed in 1994 

and 1995 for most study reaches. From 1995 

through 2001, Pool 13 had the greatest area of 

low DO concentration and exhibited a substantial 

increase between 1996 and 1997. From 1997 

through 2001, Pool 13 exhibited by far the 

largest backwater areas of low DO concentration. 

The estimated area of low DO concentration 

for Pool 13 was around 800 ha (nearly 30% of 

the backwater stratum) from 1997 to 2000 and 

approached 1,300 ha (45% of the stratum) in 

summer 2001 (Figure 5.6). The estimated area 

affected in summer for Pool 8 ranged from 3% 

to 23% (up to 400 ha in 1998). Between 60 and 

80 ha (~8%) of La Grange Pool was affected by 

low DO concentration in summer from 1996 to 

2000. That area increased somewhat in 2001 to 

about 110 ha (~10%). Pool 26 generally had the 

least estimated area affected by summer low DO 

concentration among study reaches (usually

<100 ha), but the area affected represented a 

relatively large proportion (up to 30%) of the 

backwater stratum in Pool 26. This reflects the 

relatively small proportion of the study reach 

consisting of backwaters compared to the 

northern study reaches.

Winter

In winter, the areal extent of low DO 

concentrations was much greater in the northern 

study reaches than in Pool 26 and La Grange 

Pool (there are no backwaters in Open River). 

The ranking of the northern study reaches in 

terms of the areal extent of low DO conditions 

varied among years (Figure 5.7). In 1994 and 

1995, Pool 13 exhibited the highest area of low 

DO conditions. In 1996, Pools 8 and 13 were 

similar and exhibited a greater areal extent of 
36

Figure 5.6. Extent of low dissolved oxygen (DO) concentration (<5 mg/L) observed in summer 

stratified random sampling in backwaters of the Long Term Resource Monitoring Program study 

reaches, 1993–2001. (A) Estimated area exhibiting low DO concentration, (B) proportion of sites 

that exhibited low DO concentration; Open River has no backwater stratum.

low DO conditions than Pool 4. From 1997 to 

1999, low DO was much more common in Pool 4 

than in Pools 8 or 13, which were similar to one 

another. In 2000 and 2001, the differences among 

the northern study reaches were moderate. 

The variability among the northern study 

reaches in the extent of winter low DO conditions 

suggests that local factors varying among 

years caused these differences. Differences 

in reach morphology were not a likely 

explanation because these would have remained 

approximately constant over the time scales 

examined here. Regional differences in climate, 

particularly as it affected snow and ice cover, 
37

Figure 5.7. Extent of low dissolved oxygen (DO) concentration (<5 mg/L) observed in 

winter stratified random sampling in backwaters of the Long Term Resource Monitoring 

Program study reaches, 1994–2001. (A) Estimated area of exhibiting low DO concentration, 

(B) proportion of sites that exhibited low DO concentration; Open River has no backwater 

stratum.

and current velocity in the backwaters of each of 

these study reaches were probably responsible 

for much of this variation. 

Low DO concentrations were rarely observed 

in the backwaters of Pool 26 and La Grange Pool 

in winter (Figure 5.7; Table 5.1). This is probably 

because of the minimal ice cover (which 

means oxygen exchange with the atmosphere 

is generally uninhibited) and the lower water 

temperatures (which increases oxygen solubility 

and slows oxygen consuming processes like 

microbial respiration). Although the total 

backwater area of low DO concentration is lower 

in winter than in summer, the biotic effects are 
38

potentially more severe in winter, given the more 

specific habitat requirements (i.e., low current 

velocity) for fish in winter (Knights et al. 1995). 

Summary

These results show that there were distinct 

seasonal and longitudinal patterns in DO 

concentration in the UMRS. Low surface DO 

concentrations were most frequently observed 

in summer, followed by winter. Low surface 

DO concentrations were rarely observed in 

spring or fall. Low DO concentrations in winter 

occurred more frequently in the northern study 

reaches, primarily in backwaters. In summer, 

Pool 4 and Open River rarely exhibited low DO 

concentrations, but the other four study reaches 

did at frequencies that varied among years and 

study reaches. The data represent surface DO 

concentration measurements taken during the 

day. The DO concentration exhibits diel cycles 

with minima usually occurring slightly before 

dawn and maxima occurring in the afternoon. 

In addition, DO concentration can change 

significantly with depth. As a result, the data do 

not reflect the minimum DO concentrations that 

occur at a site and provide an incomplete picture 

of the extent to which anoxia may impair UMRS 

habitat. However, the data do indicate where low 

DO concentrations are likely to be a problem. 

The patterns in surface DO concentration suggest 

that detailed studies of the distribution and 

frequency of low DO concentration would be 

most productive if focused on Pools 8 and 13 

in summer and winter. Likewise, management 

strategies, such as introducing flow to backwaters 

and using water-level manipulation to “pulse” 

water back into backwaters, might be tested or 

used in these areas.

The results illustrate important temporal and 

spatial patterns in DO concentrations. Additional 

studies addressing potential mechanisms for 

these studies would provide important additional 

understanding of the UMRS. Examples of areas 

for further inquiry include the following: What 

is the role of current velocity in determining 

backwater DO concentrations? Is there a 

current velocity threshold above which low DO 

concentrations seldom occur? How important is 

water temperature in determining the north–south 

differences in DO concentrations? Why does 

Pool 4 experience less frequent low DO 

concentrations than Pools 8 and 13? Combining 

studies designed to directly investigate questions 

such as these with the existing LTRMP 

water quality database would provide critical 

information concerning DO dynamics in the 

UMRS.
39

Chapter 6: Tributaries and Their Influence on Water Quality Spatial Patterns

by

David W. Bierman

Background

Water quality varies laterally and longitudinally 

in large river systems such as the Upper 

Mississippi River System (UMRS). The UMRS 

consists of various aquatic areas (e.g., the main 

channel, backwaters), and the water quality 

in each of these aquatic areas is dependent on 

internal processes and the degree of hydrologic 

connectivity among them. Tributary inputs can 

strongly affect lateral and longitudinal patterns 

in water quality in the UMRS. The water 

quality of each tributary is a reflection of the 

size, climate, land use, geology, hydrology, and 

chemical characteristics of its own basin (U.S. 

Geological Survey 1999). The Upper Mississippi 

River (UMR) tributaries differ greatly in their 

physical and chemical characteristics and their 

effects on the water quality of the mainstem river 

(U.S. Geological Survey 1999; Wasley 2000). 

Tributaries that drain into the UMR range from 

small intermittent streams to large, commercially 

navigable rivers such as the Illinois and Missouri 

Rivers. 

Since 1988, the Long Term Resource 

Monitoring Program (LTRMP) has monitored 

water quality on 43 UMRS tributaries. 

Tributaries to 11 of the 26 navigational pools on 

the UMR have been sampled, as well as several 

tributaries to the Open River reach of the UMR 

and La Grange Pool of the Illinois River. These 

data help identify short- and long-term trends in 

the tributaries themselves and to ascertain in-pool 

effects that may result from tributary inputs.

Contiguous backwater areas (hereafter referred 

to as backwaters) are important habitat for much 

of the UMRS biota. They serve as spawning, 

rearing, and overwintering areas for several 

species of fish (Pitlo 1992; Gent et al. 1995). 

Waterfowl use these areas heavily in spring and 

fall migrations. Abundance of vegetation and 

invertebrates is typically greater in backwaters 

than in the main channel (Sauer 2004; Yin and 

Langrehr 2005).

Construction of the lock and dam system in the 

1930s substantially affected UMRS backwaters, 

increasing their areal extent, particularly in the 

northern navigational pools (includes Pools 4, 

8 and 13; U.S. Geological Survey 1999). 

Construction of the lock and dam system has 

also greatly increased sedimentation rates 

in backwaters because of changes in natural 

hydrologic patterns (Bhowmik and Adams 

1989). Tributaries may contribute to sediment 

accumulation in backwaters when they flow 

directly into, or upstream of a backwater area. 

Tributaries typically carry high suspended solids 

loads after heavy rains. This suspended material 

settles out as the tributaries enter the quiescent 

backwaters increasing the sedimentation rates in 

these backwaters (Bhowmik and Demissie 1989). 

In this chapter, the UMRS tributaries and 

their influence are examined by looking at two 

distinct topics: (1) effects of tributary inputs on 

lateral and longitudinal patterns in water quality 

within LTRMP study reaches, and (2) differences 

among the tributaries and associated patterns in 

UMRS water quality. Specifically, we address 

three questions concerning the interactions of 

tributaries, backwaters, and the main channel of 

the UMRS:

1. To what extent can specific conductivity (a 

conservative hydrologic tracer) be used to 

track individual tributary water masses in 

the UMR? 

2. Is water quality at backwater sampling sites 

similar to that of nearby tributary sampling 

sites? Is it similar to that of adjacent main 

channel sampling sites? 

3. How does water quality vary among 

tributaries of the UMRS?
40

Methods

 The period of record covered in this chapter 

is 1993 through 2001, although data are only 

available beginning in 1998 for some tributaries. 

All water quality measurements and samples 

were collected following standard LTRMP 

water quality component procedures (Soballe 

and Fischer 2004). Only data from surface 

measurements (collected at a depth of 0.2 m) are 

included in this chapter. 

Patterns in Tributary Conductivity 

Spatial patterns in conductivity, which serves 

as a conservative hydrologic tracer, were used 

to determine the spatial extent of tributary 

influence in the six LTRMP study reaches. 

Differences often existed between specific 

conductivity of tributaries and the mainstem of 

the UMRS (Table 6.1). This situation resulted in 

spatial patterns in conductivity in LTRMP study 

reaches below the mouths of some tributaries. 

Sometimes, the spatial patterns in conductivity 

reflected tributary inputs for a considerable 

distance downstream. 

Specific conductivity readings from summer 

(late July–early August) stratified random 

sampling (SRS; Chapter 1) from each year in 

each of the six study reaches were compared 

to the mean summer specific conductivity 

(July through September 1993–2001) of major 

tributaries. The mean conductivity for each 

tributary was calculated across all years to reduce 

the effects of year-to-year variability inherent in 

tributary data. Data from summer SRS events 

were chosen because in summer water levels of 

the LTRMP study reaches and their tributaries are 

typically stable and at low flow. 

 Conductivity measurements from each summer 

SRS event in each study reach were categorized 

into quartiles and plotted by year on a map of 

the study reach. The maps were examined for 

longitudinal and lateral tributary influences by 

assessing the spatial pattern in conductivity near 

and below the tributary mouths.

To determine if similar patterns were evident 

for other water quality constituents, we plotted 

total nitrogen, total phosphorus, and total 

suspended solids, categorized by quartile, from 

spring SRS events (performed in late April–early 

May) and compared them to the 1993–2001 

spring (April through June) tributary means for 

each respective constituent for each year and 

each study reach. Data from spring sampling 

were used because nitrogen and suspended solids 

concentrations are typically relatively high in 

spring. 

Tributary Influences on Backwaters

Water quality data from tributary, backwater, 

and main channel sampling sites in relative 

proximity were analyzed for correlations among 

these sites. Appropriate data for this analysis 

were available for three locations in the UMRS: 

(1) Galena River/Sunfish Lake in Pool 12, 

(2) Rush Creek/Savanna Bay in Pool 13, and 

(3) Rock Creek/Shrickers Lake in Pool 14. Data 

for the Galena River/Sunfish Lake example were 

from 1998 to 2001 (all seasons), and data for the 

Rock Creek/Shrickers Slough example were from 

1996 to 2001 (all seasons). 

Spearman rank correlation was used to test the 

strength of bivariate relations in water quality 

constituents (i.e., total nitrogen, total phosphorus, 

and total suspended solids) between tributary and 

backwater sites and between main channel and 

backwater sites.

Longitudinal Tributary Trends

To investigate longitudinal differences 

among UMRS tributaries, 1993–2001 means 

for select tributary constituents (total nitrogen, 

total phosphorus, total suspended solids, and 

turbidity) were used and compared graphically 

to 1993–2001 means from main channel aquatic 

areas in the LTRMP study reaches. Means from 

two tributaries entering into each study reach 

were compared to the main channel means 

from the same study reach. The two tributaries 

selected from each study area had data strings 

encompassed the entire period of record and were 

major tributaries to the study reach. The means 

represent the overall mean for the period of 

record from each respective tributary (fixed-site 

data) and study reach (main channel data from 

SRS sampling) over all seasons.
41

Results and Discussion

Spatial Patterns in Specific Conductivity 

The effects of tributary inputs on spatial 

patterns in conductivity in the UMR varied 

greatly among tributaries because of differences 

in specific conductivity and discharge among 

tributaries and annual and seasonal hydrologic 

variations in the LTRMP study reaches. Pools 4, 

8, and 26 showed clear spatial patterns in 

conductivity related to tributary input in some 

years (Figures 6.1–6.3), whereas the other study 

reaches did not. 

Pool 4 

In Pool 4, the Chippewa River enters the 

lower third of the pool below Lake Pepin. 

Chippewa River water consistently exhibited 

conductivity readings that were distinctly lower 

than the adjacent Pool 4 main channel mean 

(Table 6.1). Chippewa River water remained 

close to the eastern border of the main channel 

below its discharge and appeared to track further 

downstream through the backwater complex 

in the eastern side of lower Pool 4. This spatial 

pattern was evident in 1997, 1998, and 2000, 

and somewhat evident in 1999, but was not 

seen in 1993 to 1996. Of these years, 1997 and 

2000 most clearly showed the influence of the 

Chippewa River on downstream aquatic areas 

(Figure 6.1).

Pool 8

The Black River enters the eastern portion 

of upper Pool 8, and like the Chippewa River 

in Pool 4, the Black River had conductivity 

readings consistently lower (261 μS/cm) than 

the Mississippi River main channel river water 

(429 μS/cm) at their confluence (Table 6.1). 

Generally, there was a clear east–west 

conductivity gradient in Pool 8 and it was most 

readily apparent in 1998 and 1999 (Figure 6.2), 

but is present for all years except 1994–1995.

The La Crosse River (334 μS/cm), which enters 

the eastern side of the pool at the mouth of the 

Black River, and the Root River (509 μS/cm), 

which enters the western side of the pool from 

Minnesota contribute to the lateral conductivity 

gradient in Pool 8. The lower conductivity 

readings typically observed in the eastern half of 

Pool 8 were probably because of inflows from 

the Black and La Crosse Rivers, whereas the 

higher readings in the western half of the pool 

probably reflected the influence of the Root and 

Mississippi River inflows from Lock and Dam 7.

Pool 13 

In Pool 13, the six primary tributaries all 

had mean summer conductivities higher than 

the main channel of the Mississippi River 

(424 μS/cm) and ranged from 565 μS/cm in the 

Maquoketa River to 730 μS/cm in the Elk River 

(Table 6.1). However, compared to other LTRMP 

study reaches—particularly Pools 4 and 8—

Pool 13 showed much less spatial variability in 

specific conductivity. This was probably because 

the flows of the tributaries are low relative to 

the UMR flow in Pool 13, which restricts their 

influence to small areas near their mouths. 

Pool 26

The major tributary to Pool 26 is the Illinois 

River. The Illinois River had a mean summer 

conductivity of 640 μS/cm, which was higher 

than the Pool 26 summer main channel mean of 

469 μS/cm. As a result, the Illinois River affected 

the spatial patterns in conductivity in Pool 26. 

Although this was not evident in each year, 

it was apparent in 1997, 1998, and 1999, and 

strongest in 1998 and 1999 (Figure 6.3). In these 

years, higher conductivity readings in mainstem 

Mississippi River water below the confluence of 

the Illinois River were apparent. The discharges 

of the other five tributaries to Pool 26 were 

minor compared to the Illinois River, and no 

local effects of these five tributaries on Pool 26 

conductivity were noted in this analysis. 

Open River

The portion of the Open River reach monitored 

by the LTRMP begins about 110 river miles 

below the confluence of the Missouri and 

Mississippi Rivers. Only two tributaries in this 

study area were monitored, the Big Muddy River 

and the Headwaters Diversion Channel (formerly 
42

Chippewa River

2000

1997

Chippewa River

Pool 4 N

Figure 6.1. Local influence of the Chippewa River on water quality of lower Pool 4, based upon specific conductivity 

(μS/cm) readings from summer stratified random sampling. Influence of the Chippewa River is evident from lower specific 

conductivity readings in the main channel and backwaters on the eastern side of Pool 4 below the mouth of the Chippewa 

River in 1997 and 2000. 

the Little River). No localized effects of these 

tributaries were evident in any year. This was 

most likely because of the small discharge of 

these tributaries relative to the Mississippi River.

La Grange Pool of the Illinois River 

Five tributaries to La Grange Pool of the 

Illinois River are included in the LTRMP fixedsite sampling regime. The conductivities of 

these tributaries were similar to the Illinois River 

(654 μS/cm), and conductivity in La Grange Pool 

was spatially homogeneous especially during 

years of high summer discharge (e.g., 1993 

and 1996). Mean summer conductivities for all 

five tributaries ranged from 518 μS/cm in the 

La Moines River to 666 μS/cm in the Sangamon 
43

Black River Black River

N Pool 8

1998 1999

Root

River

Root

River

Figure 6.2. Local influence of the Black River on water quality in the eastern half of Pool 8, based upon specific conductivity 

(μS/cm) from summer stratified random sampling. Influence of the Black River is evident from lower specific conductivity in 

various aquatic areas along the eastern side of Pool 8 below the mouth of the Black River compared to values in the main 

channel of the Mississippi River in 1998 and 1999. 

River (Table 6.1). Summer conductivity readings 

in La Grange Pool were typically all in the same 

quartile within any specific year. Thus, it was not 

possible to determine spatial effects of tributaries 

in this pool using conductivity as a tracer.

Total Nitrogen, Total Phosphorus, and Total 

Suspended Solids

Local influence of tributary inputs on total 

nitrogen (TN), total phosphorus (TP), and total 
44

Pool 26 N

Illinois River

Illinois River

1999

1998

Figure 6.3. Local influence of the Illinois River on main channel water quality of Pool 26, based on specific conductivity 

(μS/cm) from summer stratified random sampling. Influence of the Illinois River is evident from higher specific conductivity 

readings in main channel areas of Pool 26 below the mouth of the Illinois River in 1998 and 1999. 

suspended solids (TSS) in the Mississippi River 

were generally not seen in this analysis. It may 

be that these effects occurred at spatial and 

temporal scales that LTRMP sampling was not 

designed to detect (e.g., local effects during 

storm events). Occasionally, a local effect was 

noted for a specific parameter at a specific 

location, but no trends similar to those observed 

using conductivity intervals were obvious. 

However, concentrations of these constituents 
45

Table 6.1. Mean conductivity (μS/cm) for study reaches and selected tributaries in the Upper Mississippi and Illinois 

Rivers, 1993–2001. Data for tributaries are from the Long Term Resource Monitoring Program fixed sites in July–September. 

Data for the main channel of the study reaches are from stratified random sampling in late July–early August.

OR = Open River and LG = La Grange Pool.

Tributary

Study 

reach

Mean summer conductivity

of tributary 

Mean summer conductivity 

of study reach

Cannon River, Minnesota 4 576 453

Vermillion River, Minnesota 4 550 453

Chippewa River, Wisconsin 4 156 453

Black River, Wisconsin 8 261 429

La Crosse River, Wisconsin 8 334 429

Root River, Minnesota 8 509 429

Maquoketa River, Iowa 13 565 424

Elk River, Iowa 13 730 424

Illinois River, Illinois 26 640 469

Missouri River, Missouri OR 665 515

Big Muddy River, Illinois OR 667 515

Headwaters Diversion, Missouri OR 306 515

La Moines River, Illinois LG 518 654

Sangamon River, Illinois LG 666 654

can be altered by biological processes creating 

short-term dynamics that are not likely to be 

detected by our seasonal sampling. Because 

spatial patterns were evident in conductivity, a 

conservative tracer of tributary influence, then 

those same patterns may appear in concentrations 

of other chemical constituents. The magnitude 

of tributary discharge relative to main channel 

discharge is an important factor in determining 

whether a tributary will have substantial effect 

on spatial patterns in water quality within a study 

reach. 

Water Quality Comparison of Sampling Sites in 

Backwater, Tributary, and Main Channel Areas

Water quality relations among sets of sampling 

sites in backwater, tributary, and nearby main 

channel areas where tributaries enter into or near 

a backwater provide some information about the 

hydrologic linkages among these three areas. 

In these situations, one might expect that the 

backwater to be affected more by the tributary 

than by the main channel and that water quality 

measures in the backwater would be more closely 

correlated with the tributary.

Because of geomorphologic differences among 

study reaches in the UMRS, this configuration 

is not found in all LTRMP study reaches. It is 

most likely to occur in the Upper Impounded 

Reach (Pools 1 through 13) of the UMR, where 

tributaries enter the pools by way of braided 

side channels or directly into backwaters. It is 

not common in the Lower Impounded Reach 

(Pools 14 through 26) and does not occur in 

the Open River Reach (below the confluence 

of the Mississippi and Missouri Rivers). We 

investigated three examples of backwatertributary-main channel complexes, one each from 

Pools 12, 13, and 14. In Pool 12, Sunfish Lake 

is the backwater, the Galena River is the local 

tributary, and the Lock and Dam 11 tailwaters 

in Dubuque, Iowa, is the main channel site 

(Figure 6.4). In Pool 13, Savanna Bay is the 

backwater, Rush Creek is the local tributary, and 

the Lock and Dam 12 tailwaters in Bellevue, 

Iowa, is the main channel site (Figure 6.5). 

In Pool 14, Shrickers Lake is the backwater, 

Rock Creek is the local tributary, and a fixed 

sampling site at river mile 511.4 near Camanche, 

Iowa, is the main channel site (Figure 6.6). For 

each of these examples, data from a single fixed 
46

N

W E

S

Land

Water

Pool 12

�

L&D 11Tailwater Site

� Sunfish Lake Site

�

Galena River

Pool 12

Lock and Dam 11 Tailwater Site

Pool 12

Galena River

Sunfish Lake Site

Figure 6.4. Pool 12 of the Upper Mississippi River showing the Lock and Dam 11 tailwater site, Sunfish Lake site, and the 

Galena River. Inset map shows spatial relation of the Galena River to the Sunfish Lake site.

site from each aquatic area (backwater, tributary, 

and main channel) were analyzed. These fixed 

sites do not provide an unbiased estimate of 

concentrations of water quality constituents in 

these different aquatic areas, but can provide 

some insight into the relations that may exist 

among them.

Galena River/Sunfish Lake and Rush Creek/

Savanna Bay 

The TN, TP, and TSS concentrations at the 

Sunfish Lake site were positively correlated 

with concentrations at the Galena River site 

(tributary) and the Lock and Dam 11 tailwaters 
47

Pool 13 Land

Water

N

W E

S

�

SavannaBay Site

�

L&D 12Tailwater Site

�

Rush Creek

Savanna Bay Site

Rush Creek

Lock and Dam 12 Tailwater Site

Pool 13

Figure 6.5. Pool 13 of the Upper Mississippi River showing the Lock and Dam 12 tailwater site, Savanna Bay site, and Rush 

Creek. Inset map shows spatial relation of Rush Creek to the Savanna Bay site.

site (main channel; Figures 6.7–6.9, Panels A and 

B). For TN, concentrations were much higher 

at the tributary site than at the backwater site 

suggesting substantial dilution of tributary inputs 

in Sunfish Lake. The TP was generally higher at 

the Sunfish Lake site than at the tributary site. 

There was not a consistent difference between 

the Sunfish Lake site and the Galena River site 
48

Pool 14

Land

Water N

W E

S

�

Rock Creek

Shrickers Lake Site

�

�

M511.4 Main Channel

Border Site

Pool 14

River Mile 511.4

Main Channel Border Site

Rock Creek

Shrickers Lake Site

Figure 6.6. Pool 14 of the Upper Mississippi River showing Pool 14 main channel border fixed-site sampling, Shrickers Lake 

site, and Rock Creek. Inset map shows spatial relation of Rock Creek to the Shrickers Lake site.

for TSS. A much stronger positive relationship 

existed between the Sunfish Lake site and the 

fixed main channel site in the Lock and Dam 11 

tailwaters than between the Sunfish Lake site and 

the Galena River site (Figures 6.7–6.9; Panels 

A and B), particularly for TN and TP. Large 

differences in concentration between the main 

channel and backwater sites were not observed, 
49

Figure 6.7. Scatter plots with Spearman correlation values for total nitrogen (mg/L) at backwater, main channel, and tributary 

sites in (A) Sunfish Lake compared to Lock and Dam 11 tailwaters (Pool 12), (B) Sunfish Lake compared to Galena River 

(Pool 12), (C) Savanna Bay compared to Lock and Dam 12 tailwaters (Pool 13), (D) Savanna Bay compared to Rush Creek 

(Pool 13), (E) Shrickers Lake compared to a Pool 14 main channel site (Pool 14), and (F) Shrickers Lake compared to Rock 

Creek (Pool 14). The solid diagonal line in each chart represents the one-to-one line.
50

Figure 6.8. Scatter plots with Spearman correlation values for total phosphorus (mg/L) at backwater, main channel, and 

tributary sites in (A) Sunfish Lake compared to Lock and Dam 11 tailwaters (Pool 12), (B) Sunfish Lake compared to Galena 

River (Pool 12), (C) Savanna Bay compared to Lock and Dam 12 tailwaters (Pool 13), (D) Savanna Bay compared to Rush 

Creek (Pool 13), (E) Shrickers Lake compared to a Pool 14 main channel site (Pool 14), and (F) Shrickers Lake compared to 

Rock Creek (Pool 14). The solid diagonal line in each chart represents the one-to-one line.
51

Figure 6.9. Scatter plots with Spearman correlation values for total suspended solids (mg/L) at backwater, main channel, and 

tributary sites in (A) Sunfish Lake compared to Lock and Dam 11 tailwaters (Pool 12), (B) Sunfish Lake compared to Galena 

River (Pool 12), (C) Savanna Bay compared to Lock and Dam 12 tailwaters (Pool 13), (D) Savanna Bay compared to Rush 

Creek (Pool 13), (E) Shrickers Lake compared to a Pool 14 main channel site (Pool 14), and (F) Shrickers Lake compared to 

Rock Creek (Pool 14). The solid diagonal line in each chart represents the one-to-one line.
52

although TSS is more often higher at the Sunfish 

Lake site then at the main channel site (Figure 

6.9A).

A similar pattern occurred in Savanna Bay 

(Figures 6.7–6.9; Panels C and D). Water quality 

constituents at the Lock and Dam 12 tailwater 

site were more strongly correlated to the same 

constituents at the Savanna Bay site than those 

observed at the Rush Creek site. The TN was 

usually higher at the Rush Creek site (tributary) 

than at the Savannah Bay site (backwater). For 

TP and TSS, there were no clear differences 

between the tributary and backwater sites. The 

TN, TP, and TSS were well correlated between 

the main channel and backwater sites in this 

example, and there were no consistent differences 

in concentrations in any of these variables 

between these two sites.

For these two case studies, the correlations 

between backwater (Sunfish Lake and Savanna 

Bay) and main channel sites (tailwaters) were 

stronger for TN (Figure 6.7; Panels A and C) 

than TP (Figure 6.8, Panels A and C) and TSS 

(Figure 6.9, Panels A and C). Factors affecting 

this relationship probably included the degree of 

connectivity of the backwater to the main channel 

and the discharge of the tributary relative to the 

residence time of the receiving backwater.

Rock Creek/Shrickers Lake 

Gritters and Gould (1996) showed that water 

quality in Shrickers Lake, a backwater lake in 

Pool 14, was greatly impaired by high nutrient 

levels compared to backwaters in Pool 13. Except 

during high water conditions, Shrickers Lake 

does not receive flow from the main channel. 

However, it does receive flow from a small 

tributary, Rock Creek. Rock Creek has extremely 

elevated levels of nitrogenous compounds (i.e., 

TN, nitrate + nitrite, and ammonia nitrogen), 

below the outflow from an ammonia nitrogen 

fertilizer production plant (Gritters and Gould 

1996). Concentrations of these constituents were 

significantly elevated in Shrickers Lake as well. 

Shrickers Lake has been shown to have major 

algal blooms and die-offs and elevated levels 

of chlorophyll a, which is further evidence of 

nutrient enrichment (Gritters and Gould 1996).

Despite the evidence that water quality in 

Shrickers Lake has been greatly affected by Rock 

Creek (Gritters and Gould 1996), there was not 

a significant correlation between water quality 

constituents (TN, TP, and TSS) at the Rock 

Creek and Shrickers Lake sites (Figures 6.7–6.9, 

Panel F). As with the other backwater, tributary, 

and main channel complexes, water quality 

measurements at the Shrickers Lake site were 

more strongly correlated with the Pool 14 main 

channel site than the Rock Creek site. In this 

instance, however, the relationship between the 

main channel and backwater sites was weaker 

than those found in the Sunfish Lake and 

Savanna Bay studies. 

This analysis shows that, at these temporal 

scales, water quality at the backwater sites was 

better correlated with the main channel sites 

than the tributary fixed sites. Correlational 

analysis measures how well short-term changes 

in concentration covary over time. It does 

not measure the cumulative effect of elevated 

tributary inputs on a backwater. The cumulative 

effect of tributary inputs has been documented 

for Shrickers Lake (Gritters and Gould 1996). 

For the other backwaters, additional analyses 

would aid in understanding the role of tributary 

inputs. Specifically, backwaters receiving direct 

tributary inputs should be compared to those 

that do not receive direct tributary inputs. Such a 

comparison could indicate differences in longterm trends and differences in relationship to 

main channel conditions for backwaters receiving 

tributary inputs versus those that do not and 

would improve our understanding of the factors 

that control water quality in backwaters.

Water Quality in Tributaries of the 

Upper Mississippi and Illinois Rivers

The water quality of tributaries to the UMRS 

reflect the land use of their catchment basins 

(Wasley 2000). As a result, there is substantial 

variation in the water quality among the 

tributaries of the UMRS. Here we illustrate this 

variation by comparing water quality in a group 

of UMRS tributaries to water quality in nearby 

main channel areas (Figure 6.10). 
53

Figure 6.10. Longitudinal patterns in total nitrogen (mg/L), total phosphorus (mg/L), total suspended solids (mg/L), and turbidity (nephelometric turbidity units [NTU]) in selected tributaries to, and main channels of, the six Long Term Resource Monitoring Program study areas, based on overall means from 1993 to 2001. Note that La Grange Pool (LG) is part of the Illinois River. Open bars are the means from two major tributaries entering into each study reach and solid bars are the main channel mean in each respective study reach). OR = Open River and LG = La Grange Pool. 

(A)

Total Phosphorus (mg/L)

Total Nitrogen (mg/L)

Turbidity (NTU)

Total Suspended Solids (mg/L)

(A)
54

Upper Mississippi River Tributaries

The TN concentrations were variable among 

tributaries and no north–south trend was evident 

among the tributaries of the main channel 

(Figure 6.10A; Table 6.2). The Maquoketa River 

had the highest TN, whereas the Chippewa and 

Black Rivers had TN concentrations that were 

lower than the mainstem of the UMR. Below 

the confluence with the Missouri River, TN 

concentrations decreased, perhaps because of 

dilution from the lower TN concentrations in the 

Missouri River relative to the UMR.

The TP concentrations were less variable 

among tributaries than TN concentrations 

(Figure 6.10B; Table 6.2). The TP concentrations 

in the tributaries examined were equal or greater 

than in the UMR in 8 of 10 UMR tributaries 

examined here. The Maquoketa, Illinois, and 

Missouri Rivers had particularly high TP. The 

rest of the tributaries showed concentrations 

similar to the mainstem of the UMR. In contrast 

to TN, there was an increasing north–south 

trend in TP concentrations in the main channel 

of the LTRMP study reaches from Pool 8 to 

Open River, probably reflecting the additive 

affect of tributary inputs. Although the Missouri 

River had a comparatively low TN concentration, 

it had one of the highest TP concentrations of all 

the monitored tributaries. Phosphorus is strongly 

adsorbed to suspended particles and the high TP 

concentration observed in the Missouri River 

may be partly because of its high suspended 

sediment load (Table 6.2).

The TSS concentration is also highly variable 

among the tributaries (Figure 6.10; Table 6.2). 

The Missouri River had the highest TSS 

concentrations of any of the tributaries examined, 

followed by the Maquoketa River. Much lower 

TSS concentrations were seen in the tributaries 

to Pools 4 and 8 such as the Chippewa and 

Black Rivers. Mean turbidity and suspended 

solids levels increased downstream through the 

LTRMP study reaches (Figure 6.10; Chapter 3). 

This was probably because of the increased 

size of the drainage basin, changes in soil types 

and characteristics, and land-use practices. For 

example, flow in the Mississippi River increased 

nearly 50% below its confluence with the 

Missouri River (U.S. Geological Survey 1999). 

The mean TSS concentration of the main channel 

in Open River was nearly triple the mean main 

channel TSS concentration in Pool 26 because of 

the influence of the Missouri River (Figure 6.10).

Table 6.2. Baseflow discharge and mean concentrations of total nitrogen (TN), total phosphorus (TP), total suspended 

solids (TSS), and turbidity for selected tributaries based on fixed-site sampling by the Long Term Resource Monitoring 

Program in 1993–2001. Discharge data are 90% excedence data from Wasley (2000) for all but Spoon, Sangamon, and Missouri Rivers that were calculated separately from the U.S. Geological Survey discharge data available online at http://nwis.

waterdata.usgs.gov/il/nwis/annual/. (Accessed January 2005.) OR = Open River and LG = La Grange Pool.

Tributary Study reach

TN

(mg/L)

TP

(mg/L)

TSS 

(mg/L)

Turbidity 

(NTUa)

Discharge

(m3 s-1)

Vermillion River, Minnesota 4 3.86 0.22 28.4 21.2 0.6

Chippewa River, Wisconsin 4 1.52 0.106 15.8 9.7 96.3

Black River, Wisconsin 8 1.48 0.132 8.6 7.4 14.2

Root River, Minnesota 8 4.56 0.153 88.9 45.1 10.0

Apple River, Illinois 13 4.39 0.191 31.8 39.0 1.0

Maquoketa River, Iowa 13 7.08 0.314 138.9 108.9 10.9

Illinois River, Illinois 26 4.89 0.329 76.8 74.6 212.1

Cuivre River, Missouri 26 2.04 0.211 80.1 75.5 0.2

Missouri River, Missouri OR 2.3 0.354 307.9 198.2 1,189.3

Big Muddy River, Illinois OR 1.74 0.204 60.1 56.5 2.8

Spoon River, Illinois LG 5.42 0.251 151.4 116.8 2.6

Sangamon River, Illinois LG 4.93 0.424 151.8 89.6 11.4

a

NTU = nephelometric turbidity units.
55

Illinois River Tributaries

The two tributaries of the Illinois River—

Spoon and Sangamon Rivers—generally 

had high concentrations of TN, TP, TSS, and 

turbidity relative to the UMR (Figure 6.10). The 

Spoon River has higher TN concentration than 

all UMR tributaries except the Maquoketa River. 

The Sangamon River had higher concentrations 

of TP than any other tributaries on the UMRS. 

Both the Spoon and Sangamon Rivers had higher 

TSS concentrations than all UMR tributaries 

except the Missouri and Maquoketa Rivers. 

La Grange Pool of the Illinois River itself had 

higher TN and TP than any of the study reaches 

on the UMR reflecting the high input of its 

tributaries. Concentrations of TN, TP, and TSS, 

as well as turbidity, were similar in La Grange 

Pool of the Illinois River and the mouth of 

the Illinois River in Pool 26 of the UMR 

(Figure 6.10).

Iowa and Illinois are two of the most 

intensively farmed states in the UMR Basin, 

which was reflected in water quality of the 

tributaries that drain these two states. Of the 

tributaries monitored by the LTRMP, 12 of 

the top 15 mean TN concentrations are found 

in rivers and streams that drain land primarily 

in Iowa or Illinois. Of the 10 tributaries with 

the highest mean nitrogen concentration, Iowa 

contains six. 

Summary

As determined by analysis of conductivity 

patterns below tributary inflows, it was apparent 

that water quality conditions within a study 

reach are not spatially homogeneous. Of the 

six LTRMP study reaches, Pools 4, 8, and 26 

showed clear spatial patterns in conductivity 

related to tributary input in some years whereas 

Pool 13, Open River, and La Grange Pool did 

not. Sometimes, the direct effects of tributary 

inputs persisted for several miles downstream 

of their mouths. There were no obvious affects 

of tributaries on spatial patterns in TP, TN, or 

TSS. However, there were differences among 

tributaries in relation to these water quality 

constituents. These differences have the potential 

to affect aquatic vegetation abundance, species 

composition, and biomass. Analyses of additional 

water quality constituents, particularly dissolved 

nutrients (nitrate + nitrite, nitrogen, soluble 

reactive phosphorous) may reveal additional 

spatial patterns associated with tributary inputs.

The LTRMP SRS data were useful in assessing 

differences among study reaches and tributaries 

in various water quality constituents. However, 

SRS was not designed to address fine-scale 

patterns such as the local effects of tributaries. 

Because of the sampling density and the random 

distribution of SRS sites within each study reach, 

sufficient SRS sites are often not within the 

vicinity of tributary mouths. Spatially intensive 

sampling near the mouths of major tributaries 

may reveal local spatial patterns associated with 

tributary inputs. 

Fixed-site monitoring data were used to assess 

how water quality at backwater sites is related 

to water quality at local tributary and main 

channel sites. Analysis of the relation among 

sampling sites in the backwaters, tributaries, and 

main channel showed that concentrations of TP, 

TN, and TSS at backwater sites were correlated 

with concentration at both tributary and main 

channel sites. However, concentrations at the 

backwater sites were more strongly correlated 

with concentrations at the main channel sites than 

with concentrations at the tributary sites. Fully 

understanding the effects of tributary inputs on 

the UMRS requires calculating tributary loads 

(discharge × concentration). Including tributary 

discharge in the data collected during tributary 

sampling would facilitate calculation of loads and 

increase the use of the tributary monitoring data.
56

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dissolved oxygen, ecosystem monitoring, hydrology, Mississippi River, nitrate, nitrogen, phosphorus, 

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59 pp.

2005-T003

Multiyear synthesis of limnological data from 1993 to 2001 for the Long Term Resource 

Monitoring Program

 March 2005

This report presents a broad overview of spatial and temporal variation in the water quality of the Upper Mississippi River System (UMRS). The Long 

Term Resource Monitoring Program (LTRMP) provides a systemic perspective through the collection and analysis of monitoring data from six study 

reaches representing the upper, lower, and open river reaches of the UMRS (Upper Mississippi River: Pools 4, 8, 13, and 26, Open River [near Cape 

Girardeau, Missouri]; Illinois River: La Grange Pool). This report presents data from 1993 to 2001 (or 2002 when available) and focuses on spring and 

summer conditions. Water quality constituents (e.g., turbidity, suspended solids, chlorophyll, nutrients, and dissolved oxygen) varied among study reaches, 

aquatic area (e.g., main channel, contiguous backwaters, etc.) and seasons. For example, turbidity and suspended solids varied substantially among pools. 

Turbidity and suspended solids were much lower in lower Pool 4 than in upper Pool 4 because of the trapping of sediments by Lake Pepin, but increased 

in each of the study reaches from Pool 4 to Open River. Chlorophyll a and nutrient concentrations often differed between the main channel and contiguous backwater areas (hereafter referred to as backwaters). Summer chlorophyll a concentrations were generally higher in backwaters than in the main 

channel, and summer nitrate + nitrite (NOx) concentrations were generally lower in backwaters than in the main channel. Seasonal patterns were evident in 

chlorophyll a, nutrient, and dissolved oxygen (DO) concentrations. Main channel soluble reactive phosphorus (SRP) concentrations peaked in September 

and exhibited minima in April and May. In contrast, main channel and backwater NOx concentrations exhibited minima in fall when SRP concentrations 

are at their maximum. Seasonal chlorophyll a concentrations in main channels and backwaters show peaks in late summer and fall, with minima in winter 

and early summer. Seasonal DO patterns differed slightly among the northern (Pools 4, 8, and 13) and southern (Pool 26, Open River, La Grange Pool) 

study reaches. In the northern study reaches, DO concentrations are generally highest in spring, lowest in summer and winter, and intermediate in fall. In 

the southern study reaches, DO concentrations are highest in winter, lowest in summer, and intermediate in spring and fall. Spatial patterns within study 

reaches caused by tributary inputs were shown by the spatial patterns in specific conductivity. Of the six LTRMP study reaches, Pools 4, 8, and 26 showed 

clear spatial patterns in conductivity related to tributary input in some years whereas Pool 13, Open River, and La Grange Pool did not.
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.