U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2006–3098

 June 2006 Printed on recycled paper

Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin

Taking the Pulse of a River System: First 20 Years 

Mississippi River

Illinois River

Your doctor would not base decisions for your health care today 

on one physical examination when you were age three! You 

would reasonably expect decisions to be based on records from 

over your lifetime. Likewise, those responsible for monitoring 

the health of the Upper Mississippi River System want a more 

comprehensive way to diagnose problems and find treatment 

options. To begin developing a comprehensive view of the 

river, the five neighboring states of the Upper Mississippi River 

System and several Federal agencies formed a partnership in 

1986 to monitor river conditions and long-term trends in the 

Upper Mississippi and Illinois Rivers. 

Six monitoring targets

The overall health of a river is reflected in the health of its 

biota, such as (1) fish, (2) invertebrates (e.g., insects, worms, 

and clams), and (3) aquatic plants. The biota are affected by (4) 

water quality and (5) sedimentation, which are often influenced 

by surrounding (6) land use and land cover. All are linked. 

The Long Term Resource Monitoring Program (LTRMP) 

for the Upper Mississippi River System is the Nation’s first 

large-scale effort to determine the status and trends of these 

natural components of a large river. The mission of the LTRMP 

is to provide decision-makers with information to help them 

balance the multiple uses of the Mississippi River. We all 

benefit from commercial shipping, flood control, recreation, 

and other ecological services (e.g., biodiversity, water supply, 

biogeochemical and hydrological cycling) provided by the river. 

Our goal is to provide the information managers need to create 

a healthy large river ecosystem. 

Accomplishments

This monitoring program is at the forefront of collecting, 

sharing, and using scientifically-based information to 

understand how large rivers function and to improve river 

management. Other countries have taken notice. China, for 

example, has asked for help in learning how to monitor its 

Yangtze River.

A sample of what we’ve learned

The following pages introduce you to some of the findings 

from the monitoring program over the past 20 years. For full 

reports and graphic browsers, go to the LTRMP 

Web page at www.umesc.usgs.gov/ltrmp.html—

perhaps the world’s best source of ecological data 

on large rivers. 

Fish - good news and bad

The good news is that almost all fish species 

collected from the Upper Mississippi River 

System over the past 100 years still exist in the 

river today. That is more than a quarter of all 

Monitoring sites: Researchers 

chose six areas to represent 

conditions and habitats on the 

Upper Mississippi River System.

Researchers annually sample fish (shown here below 

Lock and Dam 7 at La Crosse, Wisconsin) to help analyze 

the status of fish populations and detect trends reflecting 

the overall health of the river.

Long Term Resource Monitoring on 

the Upper Mississippi River System
freshwater species in North America. The bad news is that 

exotic species, primarily common carp (Cyprinus carpio), make 

up about half of all the fish by weight.

Endangered Species: Since 1993, we found 39 rare, 

endangered, or threatened fish species. This provides state 

conservation officials with critical information to help recovery 

efforts for these fishes.

Exotic Species: We are tracking 11 exotic species, including 

a recent invader, Asian carp (Hypopthalmichthys spp.). The 

greatest numbers of Asian carp are presently south of Pool 13, 

but are moving upriver and expanding their range. 

watershed. Today, young native fish are more abundant in years 

when the water flow is closest to historical conditions. This 

suggests that returning this river to a more natural state would 

benefit native fish.

Invertebrates - hot topics on the river

Insects, snails, worms, and clams—to name a few—seldom 

receive publicity, but they are an important food source for 

almost all animal life in the river.

Water Quality Connection: Mayflies (Hexagenia spp.) and 

fingernail clams (Sphaeriidae) are important foods for birds and 

fish. We learned that fewer fingernail clams can live in waters 

with high suspended sediments. This suggests that management 

to reduce suspended sediments could increase fingernail clam 

levels.

One Pool Increase: We detected a slight increase in fingernail 

clams in Pool 8 from 1993 to 2004 as suspended sediments in 

the pool decreased. Other areas did not show an increase in the 

fingernail clams. 

Stable Populations: Numbers of mayflies, fingernail clams, 

and midges measured by our monitoring are similar to numbers 

reported on the river between 1952 and 1990. 

Northern Bounty: The northern study reaches (Pools 4, 8, and 

13) have more mayflies, fingernail clams, and midges than do 

the southern study reaches (Pool 26, Open River Reach, and 

La Grange Pool). 

Vegetation - double duty

Submersed aquatic plants serve wild river residents twice. 

Waterfowl and fish dine on some of the greens. Also, many fish 

hide their eggs amid the plants, their offspring use plants as 

shelter to hide from predators, and they feed on invertebrates 

that live on the plants. 

Where the Plants Grow: The abundance of submersed aquatic 

plants in different areas of the Upper Mississippi River System 

depends mainly on the water clarity, current velocity, and 

variability of water levels at that location.

Greener North: In general, aquatic plants decrease as one 

moves southward. Our studies show this is linked to the 

reduction in shallow, protected areas from north to south along 

the river.

Submersed aquatic plants, according to our studies, are more abundant in 

the shallow, protected backwaters in the northern reaches of the Mississippi 

River. 

Where the Fish Live: As anglers know, certain fish are found 

in certain habitats. Where the river has the greatest variety of 

habitats, including backwaters and side and main channels, 

is where the greatest variety of fish species will be. The 

Mississippi River north of the Open River Reach has more 

backwaters and side channels—and more sport fish—than 

farther south. We also found that water clarity, current velocity, 

and aquatic vegetation dictate differences in fish abundance.

Flood Benefits: During the extended flood of 1993 many 

fish produced more offspring than in a typical year. For some 

species, however, that does not always lead to more adult fish. 

Young fish cannot always find the conditions needed to survive 

to adulthood, especially in southern study reaches (Pool 26, 

Open River Reach, and La Grange Pool). 

Not the Same River: The Illinois River rarely flows as it 

did historically because of impoundments and changes to its 

An abundance of mayflies and fingernail clams is a sign 

of healthy river habitats.

Silver carp (Hypophthalmichthys molitrix) is only 1 of 11 exotic species 

researchers are tracking as these fish invade the Upper Mississippi River 

System. Silver carp are a concern because of their potential detrimental affect 

on fish habitats and the danger they are to boaters and others on the river 

when they leap out of the water when the water is disturbed. Photographed 

below Peoria Lock and Dam, September 2005, by Melissa Smith, Illinois River 

Biological Station-Illinois Natural History Survey.
Rehabilitation Pays Off: After building islands and reducing 

water levels during summer in Pool 8, we saw a greater growth 

of aquatic plants in 2001 through 2005. The rehabilitation work 

created new habitats and improved existing ones where plants 

could more easily grow and multiply.

Water Quality Connection: Above Lake Pepin (in Pool 4), the 

abundance of submersed aquatic plants decreased from 1998 to 

2001 and has remained low through 2005. We are unsure why, 

but we suspect the pool’s high amount of suspended sediments 

is a factor.

Exotic species: We found the exotic aquatic plants Eurasian 

watermilfoil (Myriophyllum spicatum), curly pondweed 

(Potamogeton crispus), and brittle water nymph (Najas minor), 

but they have not yet dominated the native aquatic plants.

Water Quality - so critical, so variable

Clean water helps fish, invertebrates, and plants, as well as 

migrating waterfowl to flourish in any river system. But we 

found that water quality changes substantially from north to 

south along the Upper Mississippi River System (Pool 4 to 

Open River Reach).

Decline in Quality: Our studies show that total suspended 

sediments, turbidity, and concentrations of nitrogen, 

Water stargrass (Heteranthera dubia) provides food for some waterbirds and 

homes for aquatic invertebrates consumed by a variety of fish species. 

The Long Term Resource Monitoring Program is year-round work as 

demonstrated by this crew checking water quality under the ice.

Elevation data collected before the locks and dams were created can be 

compared to present day bathymetric (water depth) data to identify areas 

where sedimentation and erosion have occurred.

 1940 1990

Filling in the Contours: Wind-generated waves sweeping 

across the open impoundments (lake-like areas on the river) 

have eroded islands and shallow areas. In deep areas of the 

impounded waters that have low current velocity, suspended 

sediment can deposit. The combination of shallower areas 

phosphorous, and chlorophyll are generally much higher in 

the southern study reaches (Pool 26, Open River Reach, and 

La Grange Pool).

Inputs off the land: Above Lake Pepin (in Pool 4), suspended 

sediments and phosphorus concentrations are high due mainly 

to inputs from the surrounding watershed and the Minnesota 

River. We found that Lake Pepin acts as a settling basin, 

greatly reducing these components and sending cleaner waters 

southward.

Algae Blooms: Summer and fall are periods of relatively 

low nitrogen and high phosphorus concentrations, conditions 

favoring growth of nuisance blooms of blue-green algae.

Channels versus Backwaters: Water quality often differs 

greatly between the main channel and backwaters. For example, 

nitrate concentrations are usually higher in the main channel, 

and algae is often more abundant in backwaters.

Changing with the Seasons: Water quality can vary 

among years and seasons. For example, main channel 

nitrate concentrations are often highest in spring, but total 

concentration varies among wet and dry years due to different 

flow levels.

Out of Oxygen: Fish cannot live in waters with low dissolved 

oxygen concentrations. Such low concentrations occur most 

commonly during summer and winter in backwaters of Pools 

4, 8, and 13, and in the main channel of La Grange Pool in 

summer. We found that low concentrations of dissolved oxygen 

are rare in other seasons and locations.

Sedimentation - moving dirt

Sediment is a natural feature of large rivers, but how it moves 

has been altered by human activities. Soil erosion from 

converting prairies and forests to agriculture and urban areas 

has increased sediment flow in the river. Impoundments such 

as dams then slow the flow and, often, more silt and sand 

accumulate than can be moved by the river, causing many 

problems. Local habitat for plants, invertebrates, and fish may 

be lost, water quality degraded, and boating endangered.
For more information, contact:

Linda Leake or Barry Johnson

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

2630 Fanta Reed Road

La Crosse, Wisconsin 54603

Phone: 608.783.6451 

Email: lleake@usgs.gov

bjohnson@usgs.gov

getting deeper and deeper areas getting shallower has resulted 

in more uniform depths in the impounded areas. With less 

variation in water depth and the loss of islands, fewer kinds of 

plants and animals can use these areas.

Carrying Silt Southward: From lower Pool 4 through 

Pool 13, sedimentation increases. We suspect this pattern is 

due to increasing amounts of suspended sediment being carried 

downstream, additions from tributary rivers, and differences in 

backwater size, depth, and shape influencing the way sediment 

is transported.

Changing Year to Year: In wet years, more water flows 

faster through the river, carrying more sediment while eroding 

previous deposits and moving all downriver. In dry years, the 

river does not have the energy to carry as much sediment. Silt 

and sand will settle out of the water, accumulating locally.

Land Cover - a mirror of time

From north to south, the dominant use and appearance of the 

Upper Mississippi River System changes considerably. 

The upper portion, from the Twin Cities, Minnesota, to 

Clinton, Iowa (Pools 1–13), is mainly open water (40%) and 

floodplain forest (21%) with a variety of other habitat types and 

relatively little agriculture (5%). 

In the middle portion, from Clinton, Iowa, to St. Louis, 

Missouri (Pools 14–26), agriculture becomes more 

common (48%), while open water (22%) and floodplain 

forests (17%) decrease. 

The lower portion, including the Open River Reach from 

St. Louis, Missouri, to Cairo, Illinois, and the Illinois River 

pools, is mainly agricultural (51%) with many levees, extensive 

channelization, and little variety in habitat. Open water (16%) 

and floodplain forest (16%) continue to decrease.

Flood Victims in Nature: The large floods in 1993, 1997, 

and 2001 swept away shallow-rooted plant species such as 

arrowhead (Sagittaria), water lily (Nymphaea) and lotus 

(Nelumbo), and killed trees by drowning their roots. Since 2001, 

we have found a regrowth of aquatic plants in the northern 

pools. 

Open Water Replaces Marshes: Among habitat types, open 

water has increased the most in the northern pools since 1989. 

This change has come at the expense primarily of deep marshes 

that once contained important plants such as arrowhead, lotus, 

water lily, and submersed vegetation. Habitat enhancement 

projects are helping to restore these plants in many sections of 

the river.

Shrinking Forests: Before European settlement, forests 

covered much of the floodplain. Now only remnants remain 

and they continue to shrink. Recent decreases may be due to the 

1993 flood and inadequate growth of new trees as the mature 

trees die. Invasive nonforest species such as reed canary grass 

are also inhibiting reforestation. 

Contacts:

U.S. Geological Survey

Upper Midwest Environmental Sciences Center

Phone: (608) 783-6451

U.S. Army Corps of Engineers

Phone: (309) 794-5857

U.S. Fish and Wildlife Service

Phone: (612) 713-5178

Illinois Department of Natural Resources

Phone: (217) 785-8264

Iowa Department of Natural Resources

Phone: (515) 281-6976

Minnesota Department of Natural Resources

Phone: (507) 280-5058

Missouri Department of Conservation

Phone: (573) 522-4115

Wisconsin Department of Natural Resources

Phone: (608) 785-9000

U.S. Environmental Protection Agency

Phone: (312) 886-6872

A century of changes in land cover can be traced with these maps at what is now Pool 13 on the Upper Mississippi River. Before the locks and dams and 

increased population, forests filled much of the flood plain (left). Now there is more open water, less forest, and more submerged aquatic plants.

15-Class Legend

Open Water

Submerged Aquatic Vegetation

Rooted Floating Aquatics

Deep Marsh

Shallow Marsh

Wet Meadow

Sand/Mud

Grass/Forbs

Scrub/Shrub

Wet Shrub

Wet Forest

Upland Forest

Agriculture

Road/Levee

Developed

No Photo Coverage/Unknown

gqg

Rooted Floating Aquatics

Deep Marsh

Shallow Marsh

Wet Meadow

Sand/Mud

Grass/Forbs

Scrub/Shrub

Wet Shrub

Wet Forest

Upland Forest

Agriculture

Road/Levee

Developed

No Photo Coverage/Unknown