MMSD Watercourse Corridor Study: Geomorphology and Sediment Studies Related to Stream and Estuary Rehabilitation

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Geomorphology and sediment studies related to stream and estuary rehabilitation consist of four subproject areas: pre- and post-rehabilitation assessments, characterization of stream network-based habitat units for habitat critical to aquatic organisms, characterization of the Milwaukee River estuary, and instream sources of sediment and phosphorus.

During the current 5-year study period for Phase V (2016-2020) of the Milwaukee Metropolitan Sewerage District (MMSD) Watercourse Corridor Study, the following four topics are being addressed by one or more USGS subprojects:

1.    Ecological Assessments and Trends
2.    Geomorphology and Sediment Studies Related to Stream and Estuary Rehabilitation
       a.    Pre- and Post-rehabilitation Stream Geomorphic and Habitat Assessments
       b.    Characterization of Potential Channel Habitat Units through Stream Network-Wide Geomorphic Characterization
       c.    Milwaukee River Estuary Geomorphology, Hydrodynamics, and Habitat
       d.    Instream Sources of Sediment and Phosphorus and Effects on Stream and Estuary Rehabilitation
3.    Contaminants in Water and Sediment
4.    Continuous Real-Time Streamflow

This webpage focuses on topic 2. Geomorphology and Sediment Studies Related to Stream and Estuary Rehabilitation.

 

Geomorphology and sediment studies related to stream and estuary rehabilitation consist of four subproject areas: pre- and post-rehabilitation assessments, characterization of stream network-based habitat units for habitat critical to aquatic organisms, characterization of the Milwaukee River estuary, and instream sources of sediment and phosphorus. The work is done in consultation with MMSD watercourse engineers to assist with planning, design, and evaluation of rehabilitation projects. Much of the rehabilitation work involves removal of concrete-lined channels.

 

2a. Pre- and Post Rehabilitation Stream Geomorphic and Habitat Assessments

BACKGROUND

Field assessments of the physical habitat and geomorphic aspects of streams in the MMSD service area have been an integral component of ecological assessments throughout the first four phases of the Corridor Study. These studies have played a key role in understanding of water resources and interpretation of water-quality data in the area, as well as documenting the effectiveness of rehabilitation projects. Habitat assessments at sites are based on USGS NAWQA protocols (Fitzpatrick and others, 1998), and serve as a complement to ecological data collection efforts (Moulton and others, 2002). The key indicators of stream physical habitat are channel dimensions, channel slope, streambed sediment size, habitat complexity and cover, vegetation cover and structure in the riparian area (along the stream banks), channel-riparian connection, and anthropogenic alteration (Fitzpatrick and Peppler, 2007; 2010). Understanding the lateral connection between channel geomorphology and riparian habitat is especially important for native birds, mammals, reptiles, and insects. Longitudinal as well as lateral connections along stream corridors are also important in terms of fish passage and long-term rehabilitation goals and in the context and limitations of providing safe flood management and public access.

OBJECTIVES

Objectives of the pre- and post- rehabilitation assessments include the consistent use of quantitative field-based assessments to 1) evaluate the success of rehabilitation projects, with data for comparison of channel geometry, bedforms, channel and bank stability, substrates, and riparian vegetation conditions, and 2) to provide technical assistance to MMSD for rehabilitation plans.

APPROACH

Field assessments of physical habitat and geomorphic characteristics will be done at new sites  that are planned or have had recent stream rehabilitation work by MMSD. Assessments will be completed at about three sites per year, with location and timing dependent on rehabilitation work. At about 10 urban analog (least disturbed) sites, invertebrate community sampling was completed in 2017 by USGS to augment Phase IV stream habitat assessments. Additional quantitative measurements of bank erosion, stream sediment type, fine sediment deposition, pools, large wood, and artificial habitat or stabilization features have been added to the original habitat protocols (Young and others 2015; Fitzpatrick and others, 2016). Riparian vegetation surveys were also added and transect data are connected laterally to channel and aquatic habitat transects.

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2b. Characterization of Potential Channel Habitat Units Through Stream Network-Wide Geomorphic Characterization

BACKGROUND

A geomorphic-based framework of habitat units for streams in the Milwaukee River watershed is being developed in a geographic information system (GIS) to incorporate the geomorphic and riparian land cover features that form the backbone of aquatic habitat features and functions in the MMSD planning area. This framework provides the background needed to analyze rehabilitation alternatives in terms of the historic natural channel and riparian conditions.

OBJECTIVES

The objectives of this study are to characterize and classify the streams in the MMSD area according to their stream order, slope, riparian geologic setting and soils, and pre-settlement vegetative cover. The resulting GIS layer can be used for rehabilitation planning and quantifying habitat units along the stream corridors. The goal is to increase connectivity across a diverse set of habitats that were present prior to urbanization.

APPROACH

Assessment methods were adopted the Los Angeles River Ecosystem Restoration (U.S. Army Corps of Engineers and Northwest Habitat Institute, 2013) and began in 2016. The Wisconsin Department of Natural Resources (WDNR) stream network was overlaid with County lidar-based digital elevation model data to extract stream slope for each stream segment (WDNR, 2014). The segments are subsequently classified by their stream order (size) (Strahler, 1957), sinuosity, and potential erodibility. For the surrounding 30-m buffer, land cover, surficial geology, soils, pre-settlement vegetation, and wetlands are mapped. An additional layer for pre-settlement stream locations, obtained from MMSD, is also included for comparison. A pilot study was done by Smith (2016). A final GIS layer will be completed in 2019.

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Map showing slope, surficial geology, and soil units of a Underwood Creek stream reach

Example map showing overlays of stream slope, surficial geology, and pre-EuroAmerican settlement 1836 Public Land Survey (PLS) streams and wetlands for Underwood Creek, Wis.

Data citations:

Original vegetation: Wisconsin Department of Natural Resources, 2017

Original vegetation polygons: Wisconsin Deparptment of Natural Resources, Madison, WI.

https://www.arcgis.com/sharing/rest/content/items/3e952715b0d549c39cd8e26b4b274a0c/info/metadata/metadata.xml?format=default&output=html, 1:500, 000 scale

Slopes from Milwaukee County lidar-based DEM: Milwaukee County Land Information Office, 2010, Coutnywide LiDAR 5ft DEM Smoothed: https://county.milwaukee.gov/EN/Administrative-Services/Land-Information-Office/GIS-Data/Data-Download-Form

Surficial geology: WDNR, 2011, Surficial Deposits, in Ecological Landscapes of Wisconsin Handbook 1805.1, https://dnr.wi.gov/topic/landscapes/documents/StateMaps/Map_S12_Surficial_Deposits.pdf scale 1:500,000.

Streams: WDNR, 2008, Rivers and streams hydrography, 1:24,000 scale, :http://dnr.wi.gov/maps/gis/datahydro.html

 

2c. Milwaukee River Estuary Geomorphology, Hydrodynamics, and Habitat

BACKGROUND

This effort will include development of a physical habitat framework for large habitat types based on the Milwaukee Harbor Estuary Remedial Action Plan (WDNR, 2014), including effects from multidirectional currents and seiche effects associated with the mixing of river flows with Lake Michigan backwater. The framework will build off of existing nearshore and estuary frameworks developed for other areas of the Great Lakes as well as a fish habitat study by UW-Milwaukee (Dow, 2018).

Milwaukee River Estuary, March 2016

Milwaukee River Estuary, March 2016 (Credit: Faith Fitzpatrick, USGS)

OBJECTIVES

The goal of the USGS/MMSD Milwaukee Harbor Estuary habitat study is to develop a pilot framework for baseline assessment, mapping, and rehabilitation evaluation of physical habitat in the Milwaukee Harbor Estuary under MMSD jurisdiction. This framework will be linked to the binational efforts for development of a baseline habitat assessment for the Great Lakes and for the Great Lakes Restoration Initiative. It will focus specifically on the estuary/river mouth mixing zone under the influence of both varying river flows and seiche-related currents and water-level fluctuations.

APPROACH

The pilot framework will reflect habitat measurement protocols and hydrodynamic data and modeling related to the development of the updated Great Lakes ecological and habitat indicators previously piloted by the Great Lakes Science Advisory Board, Research Coordination Committee in 2016; NOAA’s coastal and estuarine habitat classification (Allee and others, 2000), and the European Environment Agency’s habitat classification scheme and interactive mapper for marine environments in the European Nature Information System (EUNIS) European Marine Observation and Data Network (EMODnet; Davies and others, 2004). The four recommended coastal marine habitat classification frameworks from Lund and Wilbur (2007) will be evaluated. The habitat assessment will tentatively reflect a combination of the following characteristics: substrate texture and layering, bedforms and bedrock, sediment mobility; wave/current energy, water-level and depth variability in terms annual and seasonal lake level statistics and regulatory levels. Much of the physical data has been collected and mapped by Dow (2018). The assessment will also incorporate a range of hourly seiche variations; natural and artificial structures; shore ice and ice jams, water temperature and sediment oxygenation, and beds of rooted aquatic and wetland vegetation.

The study approach will emphasize integration of available substrate/sediment data maps from the University of Wisconsin-Milwaukee Freshwater Institute (Dow, 2018); hydrodynamic models, such as the Milwaukee Harbor Estuary Hydrodynamic and Bacteria Modeling, USGS velocity, stage, temperature, and flow data (U.S. Geological Survey, 2018), and any new hydrodynamic models that are developed by the Global Water Center. Project personnel will work closely with others involved in field surveys and mapping in the Estuary, including the Technical Advisory Team for the Milwaukee Area of Concern as well as those conducting similar studies for the St. Louis River National Estuarine Research Reserve. In 2019, a meeting will be convened to bring together those working on physical data and modeling in the Estuary. In 2020, maps will be published as an interactive web mapper. Any new data will be published in the USGS ScienceBase and referenced in the USGS Science in the Great Lakes Mapper (SiGL). The pilot estuarine habitat classification will be published as a USGS Scientific Investigations Report. 

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Map dissolved oxygen and turbidity Milwaukee River

Map of dissolved oxygen and turbidity along the Milwaukee River. (Credit: Faith Fitzpatrick, USGS)

These data are preliminary or provisional and are subject to revision. They are being provided to meet the need for timely best science.

 

2d. Instream Sources of Sediment and Phosphorus and Effects on Stream and Estuary Rehabilitation

BACKGROUND

Fine-grained sediment and associated contaminants and nutrients are pollutants in streams and estuaries, including urban and agricultural watersheds in the Milwaukee River Basin. Rehabilitated urban streams may still have sediment-related impairments from upstream nonpoint sources of agricultural fields and pasture, construction sites, roads and parking lots, and eroding stream banks. These include the physical presence of the sediment that can cause ecological harm such as burial and scour, as well as chemical contamination (for example, heavy metals and PAHs) and excessive nutrient loading (especially phosphorus, which can cause harmful algal blooms in streams, estuaries, and nearshore areas). Additionally, excessive coarse sediment and large wood jams, possibly from bank erosion, are of concern in urban streams with narrow riparian corridors. In the Kinnickinnic River there are multiple sources for sediment and sediment related contaminants, including street and parking lot runoff and streambank erosion. There are ongoing, complementary studies by the WDNR, MMSD, and USGS of the potential sources of sediment-bound PAHs to the mouth of the Kinnickinnic River in areas that were recently dredged as part of the Milwaukee River Area of Concern. 

OBJECTIVES

The objective of this study is to determine the major sources of sediment, sediment-related PAHs, and phosphorus associated with habitat degradation and channel instability in the Kinnickinnic River watershed. Of particular interest is sediment and sediment-bound phosphorus contributed from eroding tributary streambanks to the concrete-lined main stem.

APPROACH

This study will select a pilot watershed in the MMSD area (likely the Kinnickinnic River) in 2019 to examine the linkage of sediment and related contaminants to specific source areas and their downstream effects on habitat. Suspended sediment and recently deposited sediment will be sampled after major storm events using automatic and manual samplers. Sediment samples from nonpoint source areas including streets and parking lots, constructions sites, wooded riparian areas, and eroding stream banks will also be collected. Stream banks eroding parent material (glacial till, etc.) will be distinguished from those eroding historical alluvium or fill left by streams, as they may have different contaminant and phosphorus signatures. Locations for target sample collection will be integrated with ecological, restoration evaluation, and urban analog reaches, and those identified as problem areas. Suspended sediment will be collected at the gage location as well as potentially 2-3 upstream locations. An integrated sediment budget/sediment fingerprinting approach for identification of sediment sources for Total Maximum Daily Loads (TMDLs) will be used (Cashman et al., 2018; Gellis et al., 2016; Lambda et al., 2015). Sample analyses will include a suite of trace elements, sediment-related PAHs, and phosphorus, as well as conservative isotopes.

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