River-Corridor Habitat Dynamics Research
Lower Missouri River

Intensive management of the Missouri River for navigation, flood control, and power generation has resulted in dramatic physical changes to the river corridor.  Historically, the Missouri River was characterized by a shifting, braided channel and abundant unvegetated sandbars.  The shifting channel provided a wide variety of hydraulic environments and a large quantity of connected and non-connected off-channel water bodies.  Beginning in the early 1800’s and continuing to the present, the channel of the lower Missouri River (downstream from Sioux City, Iowa) has been trained into a fast, deep, single-thread channel.  Wing dikes now concentrate the flow and revetments and levees keep the channel in place and disconnect it from the floodplain.  In addition, reservoir regulation of the Missouri River has substantially changed the annual hydrograph, sediment loads, temperature regime, and nutrient budgets.


While changes to the Missouri River have resulted in broad social and economic benefits, they have also been associated with degradation of river-corridor habitats and diminished populations of native fish and wildlife species.  Today, Missouri River stakeholders are seeking ways to restore some natural ecosystem benefits without compromising traditional economic uses of the river and flood plain.

Research Objectives

The objective of the project is to improve the scientific basis for ecological restoration of large rivers.   Ecological restoration seeks to restore the physical, biological, and chemical processes of a formerly functional ecosystem.  Efforts to restore the Missouri River have focused mostly on restoring some of the hydrologic and geomorphic characteristics of the former river, with the assumption that ecosystem processes will follow.  Considerable uncertainty exists in the restoration process, including fundamental questions about the physical system: how do hydrologic and geomorphic characteristics combine to create the right kinds of habitats at the right times and places, and how does the physical template of habitats vary over time as the river erodes and deposits sediments? 

The project is designed to improve understanding of three aspects of habitat:

Measuring and Modeling the River

The Missouri River-Corridor Habitat Dynamics Project emphasizes quantitative measurement of fundamental physical processes in the river at scales meaningful to habitat assessment. The deep, swift, and muddy Missouri River presents considerable challenges to making basic measurements of the river, including depth, velocity, substrate, and elevation characteristics.  We use  an integrated hydro-acoustic mapping system that combines precision positioning using real-time kinematic global positioning (RTK GPS), survey-grade echosounding, a bed-material classification system, and acoustic Doppler current profiling.  Data from the acoustic acquisition system are used to create maps of the river, including that can be used to assess habitat availability. 

Because habitat varies with discharge, assessment of habitat availability has to account for discharge variation, either by focusing on a single index discharge or by evaluating habitat over a range of discharges.   We use the hydro-acoustic maps to construct, calibrate, and validate 1- and 2-dimensional hydraulic models.  The hydraulic models allow us to evaluate habitat availability with varying discharge.

Establishing the link to how fish use the habitat is critical but challenging because of difficulties in locating fish in the deep, turbid water of the Missouri River.  Increasingly, we are working with fish ecologists to track fish that are tagged with acoustic or radiotelemetry devices.  Telemetry provides point locations from which habitat patches can be defined and mapped.  The mapped patches quantify characteristics of used habitats, unused habitats, and their spatial variability.  Explicitly linking habitat availability to habitat use allows fish ecologists to evaluate which habitats the fish select under various conditions.  Collaborations currently include mapping of pallid sturgeon, Asian carp, and flathead catfish habitats.

Adaptive Management: Linking Science to Management Decisions

The adaptive management concept provides a framework for scientists to interact substantively with managing agencies and stakeholders.  Scientists can serve to inform management objectives, to help design the investigative framework for performance assessment, and to help in interpretation and application of new understanding to management decisions.  Adaptive management can also provide a priceless service to scientists by supporting field-scale experiments that would otherwise be difficult or impossible to carry out.

Much of the research carried out by River Corridor Habitat Dynamics scientists relates to ongoing adaptive management of the Lower Missouri River.  Monitoring and assessment of geomorphic and ecologic changes to side-channel chutes, wetlands, and within-channel rehabilitation projects supports multi-agency adaptive rehabilitation efforts.   One example is monitoring and assessment of shallow-water habitat projects another is assessment of factors determining long-term ecological functions of side channel chutes. 

Scientists ensure that their information is made available to managers, stakeholders, and the general public by participating in management forums like the Missouri River Federal Roundtable, disseminating scientific results to the public in accessible formats, and actively participating in regional, Missouri River conferences.

Core Scientists


Core scientists are involved in extensive research collaborations with the Columbia Environmental Research Center, with the Missouri Cooperative Research Unit, Missouri District, USGS Water Resources Discipline, USGS Columbia River Fisheries Laboratory, National Park Service, U.S. Fish and Wildlife Service,  University of Missouri, Southern Illinois University, University of Texas-Arlington, and University of Illinois.

Current Studies

The following studies are currently being pursued River Corridor Habitat Dynamics research.

Online project publications

Jacobson, R.B., and Galat, D.L., in review, Flow and form in rehabilitation of large-river ecosystems – an example from the Lower Missouri River: in review, special issue of journal Geomorphology, Linking Geomorphology and Ecology.

Jacobson, R.B., Elliott, C.M., and Johnson, H.E., in review, Rehabilitated shallow-water habitat evaluation, Lower Missouri River: U.S. Geological Survey Open-file report series.

Jacobson, R.B., Johnson, H.E., Laustrup, M.S., D’Urso, G.J., and Reuter, J.M., 2004, Physical habitat dynamics in four side-channel chutes, Lower Missouri River: U.S. Geological Survey Open-File Report 2004-1071, 60 p, On CD-ROM or online at: http://infolink.cr.usgs.gov/RSB/USGS_OFR_2004-1071/index.htm

Elliott, C.M., Jacobson, R.B., and DeLonay, A.J., 2004, Physical aquatic habitat assessment, Fort Randall segment of the Missouri River, Nebraska and South Dakota: U.S. Geological Survey Open-Filer Report 2004-1060 80 p. On CD-ROM or online at: http://infolink.cr.usgs.gov/RSB/USGS_OFR_2004-1060/index.htm

Jacobson, R.B., and Heuser, J.L., 2002, Visualization of flow alternatives, Lower Missouri River, U.S. Geological Survey Open-file Report 02-122, Online at:  http://www.cerc.usgs.gov/rss/visualize/visualize.htm

Jacobson, R.B., Laustrup, M.L., and Reuter, J.M., 2002, Habitat assessment, Missouri River at Hermann, Missouri:  U.S. Geological Survey Open-file Report 02-32, 22 p., 181 oversize maps.  On CD-ROM or online at: http://www.cerc.usgs.gov/pubs/Moriver/herm_hab.htm

Jacobson, R.B. and Laustrup, M.L., 2002, Habitat assessment for pallid sturgeon overwintering surveys, Lower Missouri River: U.S. Geological Survey Online report: http://www.cerc.usgs.gov/pubs/center/pdfDocs/micra_whole.pdf,

For more information, contact:

Robert B. Jacobson, Ph.D.
Research Hydrologist
U.S. Geological Survey - CERC
4200 New Haven Road
Columbia, MO 65201

Publications online at:


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