Black River, Cawley and Rock Creeks,O'Neill and Cunningham Creeks Watershed (BR09)
Black River, Cawley and Rock Creeks,O'Neill and Cunningham Creeks Watershed (BR09)
Black River (1676700)
7.62 Miles
103.21 - 110.83
Natural Community
Natural communities (stream and lake natural communities) represent model results that use predicted flow and temperature based on landscape features and related assumptions. Ranges of flow and temperature associated with specific aquatic life communities (fish, macroinvertebrates) help biologists identify appropriate resource management goals. Wisconsin Natural Communities.
Warm Mainstem, Cool-Cold Mainstem
Year Last Monitored
This is the most recent date of monitoring data stored in SWIMS. Additional surveys for fish and habitat may be available subsequent to this date.
This river is impaired
Impairment Unknown
Total Phosphorus
Trout Water 
Trout Waters are represented by Class I, Class II or Class III waters. These classes have specific ecological characteristics and management actions associated with them. For more information regarding Trout Classifications, see the Fisheries Trout Class Webpages.
Outstanding or Exceptional 
Wisconsin has designated many of the state's highest quality waters as Outstanding Resource Waters (ORWs) or Exceptional Resource Waters (ERWs). Waters designated as ORW or ERW are surface waters which provide outstanding recreational opportunities, support valuable fisheries and wildlife habitat, have good water quality, and are not significantly impacted by human activities. ORW and ERW status identifies waters that the State of Wisconsin has determined warrant additional protection from the effects of pollution. These designations are intended to meet federal Clean Water Act obligations requiring Wisconsin to adopt an 'antidegradation' policy that is designed to prevent any lowering of water quality - especially in those waters having significant ecological or cultural value.
Impaired Water 
A water is polluted or 'impaired' if it does not support full use by humans, wildlife, fish and other aquatic life and it is shown that one or more of the pollutant criteria are not met.

Fish and Aquatic Life

Current Use
The use the water currently supports. This is not a designation or classification; it is based on the current condition of the water. Information in this column is not designed for, and should not be used for, regulatory purposes.
Supported Aquatic Life
Waters that support fish and aquatic life communities (healthy biological communities).
Attainable Use
The use that the investigator believes the water could achieve through managing "controllable" sources. Beaver dams, hydroelectric dams, low gradient streams, and naturally occurring low flows are generally not considered controllable. The attainable use may be the same as the current use or it may be higher.
Supported Aquatic Life
Waters that support fish and aquatic life communities (healthy biological communities).
Designated Use
This is the water classification legally recognized by NR102 and NR104, Wis. Adm. Code. The classification determines water quality criteria and effluent limits. Waters obtain designated uses through classification procedures.
Default FAL
Fish and Aquatic Life - Default Waters do not have a specific use designation subcategory but are considered fishable, swimmable waters.


The portion of Black River within the Lower Black River watershed (BR01) contains areas of eroding sandy banks. Approximately half of the river miles in this watershed flow through the Van Loon State Wildlife Area and the Upper Mississippi River Fish and Wildlife Refuge.

The Melrose Wastewater Treatment Plant discharges to the Black River. This plant had problems meeting biochemical oxygen demand (BOD) limits. The village was placed on a sewer extension moratorium in August 1994 for this reason. Adjustments to treatment plant operations have improved plant performance, which led to the lifting of the sewer extension ban in October, 1996 (Pietz).

The Black River Falls wastewater treatment plant treats waste from the communities of Brockway and Black River Falls and discharges treated effluent below the dam. The plant has exceeded the permit limitations for certain metal concentrations. An aggressive water supply system which leaches metals from pipes was determined to be a major source of the problem. Steps to reduce pipe corrosion in the water supply system reduced metal levels at the wastewater treatment plant (Pietz).

A new Neillsville wastewater treatment plant was constructed and discharging in 1997. The old wastewater treatment plant was organically overloaded. The new plant design effectively treats organic wastes while decreasing its design flow. The discharge to the Black River will not change (Pietz).

From: Koperksi, Cindy. 1999. Black River Water Quality Management Plan (draft). Wisconsin Department of Natural Resources, Madison, WI.

Date  1999

Author  Cynthia Koperski


The portion of Black River in the Popple River watershed (BR11) is characteristically rocky. Filamentous algae is commonly seen on rocks. The river supports a warm water sport fishery. During low flow, the river is nearly impossible to navigate; however, a few large pools support fish life (Talley).

Owen has a permit to discharge treated wastewater to the Black River. The Owen WWTP receives waste from neighboring city of Withee. Both communities reported by-passing raw sewage to the Black River during rain events due to overloading of water volumes at lift stations. To solve this problem, both Owen and Withee are sealing sanitary sewer manhole covers to prevent stormwater from entering the system and sealing off other direct connections of stormwater. Replacing and rehabilitating sanitary sewer lines is also being done on a continual basis (Pietz).

A fish consumption advisory exists for fish in the Black River south of HWY 29/73. Mercury detected in a variety of fish prompted the DNR to list the river in its advisory (WDNR, 1997). In order to update the advisory database and track mercury concentration trends, game fish should be collected from the portion of Black River in this watershed (Amrhein).

Black and Little Black River watershed (BR13) - The first thirteen miles of the Black River is a class II trout stream. The river becomes class III trout for the five mile segment above Medford. Below Medford, the Black River becomes a warm water sport fishery. Low dissolved oxygen concentrations have been periodically documented in the trout stream segments above Medford. Wetland drainage is believed to be at least partially responsible. The Black River trout population has shown a dramatic decline in recent years. Nonpoint source impacts are suspected to be the cause (Lealos, 1997). Below Medford, a mercury advisory exists for walleye and smallmouth bass (WDNR).

The Chelsea Sanitary District constructed a community wastewater treatment system to replace failing residential septic systems. The system consists of two septic tanks operated in series, a recirculating sand filter, and a chlorination-dechlorination disinfection unit. The residential septic tanks have been abandoned (Franson). The discharge from this facility is to the Black River in Taylor County.

From: Koperksi, Cindy. 1999. Black River Water Quality Management Plan (draft). Wisconsin Department of Natural Resources, Madison, WI.

Date  1999

Author  Cynthia Koperski


The portion of the Black River within the Cawley and Rock Creeks watershed (BR10) contains both long pools and long, rugged riffle areas. River substrate is mostly comprised of gravel, cobble and boulders. Filamentous algae on rocks is common (Talley).

A fish consumption advisory exists for the entire length of the Black River contained in this watershed (WDNR, 1997). Mercury levels detected at high levels in a variety of fish species prompted the DNR to include this portion of the Black River. Further discussion of this issue can be found in the Black River main stem discussion of this report.

In order to meet their phosphorous limit, Grassland Dairy built a new wastewater treatment plant that came on line in 1998. The facility continues to discharge to the Black River via the Loyal wastewater treatment plant discharge pipe.

From: Koperksi, Cindy. 1999. Black River Water Quality Management Plan (draft). Wisconsin Department of Natural Resources, Madison, WI.

Date  1999

Author  Cynthia Koperski

Historical Description

The major stream system in Clark County. It enters from the north and flows southward into Arbutus Lake. It is a soft water stream having a medium brown color. The river is characterized by long sluggish pools followed by swift riffle areas. Boulder is one of the dominant bottom types in the lower one-half of its length in Clark County. Some of the stream passes through steep-sided, gorge-like areas that enhance its beauty. About 75 percent of the watershed has been cleared for agricultural uses. Muskellunge, northern pike, walleye, largemouth bass, smallmouth bass, catfish, and panfish constitute the sport fishery. It is one of the better smallmouth bass streams in west central Wisconsin. Carp are present. Furbearers and waterfowl are present and the latter provide some jump shooting in autumn. Light boat traffic is possible on the entire river in Clark County, but even during normal water level periods it is necessary to portage around some of the riffle areas. Inadequately treated wastewater from gravel washing operations has been discharged into the river resulting in turbid water in the areas of discharge near Withee and Greenwood. There is one picnic site and one park area. Thelatter has an unimproved boat landing. About 2.1 miles of shoreline are in public ownership. Several roads cross the stream and access is also possible by boat from Arbutus Lake.

Black River T23N, R3W, S24, Surface Acres 1,561, Miles = 54.1, Gradient = 8.6 feet per mile.

From: Klick, Thomas A. and C.W. Threinen, 1965. Surface Water Resources of Clark County: Lake and Stream Classification Project. Wisconsin Conservation Department, Madison, WI.

Date  1965

Author   Aquatic Biologist

Black River, Cawley and Rock Creeks,O'Neill and Cunningham Creeks Watershed (BR09) Fish and Aquatic LifeBlack River, Cawley and Rock Creeks,O'Neill and Cunningham Creeks Watershed (BR09) RecreationBlack River, Cawley and Rock Creeks,O'Neill and Cunningham Creeks Watershed (BR09) Fish Consumption

General Condition

The Black River, in this watershed, currently receives two discharges, the Greenwood WWTP and a combined discharge from Grassland Dairy and the Loyal WWTP. During a high flow period in April, 1990, macroinvertebrate samples were collected from the Black River below the Loyal/Grassland Dairy discharge. The analysis of the macroinvertebrate samples resulted in an index of good to fair water quality with some organic pollution present (WDNR, 1990).

For approximately a seven mile stretch downstream of Rock Creek, the Black River is listed as a total maximum daily load (TMDL) site. Water chemistry data documents that some water quality standards have not been met. The sources of pollution that contribute to this situation include both point source and non-point source discharges. The problem has only been recorded during low flow conditions. Because the two outfalls to the Black River are relatively close, it is uncertain whether an overlap of effluent mixing zones occurs. Ammonia is one regulated compound that can have immediate deleterious effects to the biological community of the Black River. A 1993 study to determine ammonia mixing characteristics of Greenwood WWTP with the Loyal/Grassland Dairy discharge was inconclusive due to a combination of high streamflow and low effluent ammonia levels at Greenwood (La Liberte, 1996).

The Greenwood WWTP underwent a facility upgrade which increased the design flow to 0.524 million gallons/day. The facility discharged higher than allowed suspended solids before the plant upgrade. The City now operates an industrial pretreatment plant, which has decreased suspended solids reaching the Greenwood treatment plant.

Date  1999

Author   Aquatic Biologist

Impaired Waters

For surface water quality assessment purposes the Black River is defined by 12 segments.

Black River from Great River State Trail to the La Crosse-Trempealeau-Jackson county line (miles 14.52 to 37.01) was put on the Impaired Waters List in the 1998 cycle for Mercury and PCBs in fish tissue. This segment of the Black River was evaluated every two-year cycle from 2012 to 2022; phosphorus levels were found to be too high and was added to the list.

Black River from La Crosse-Trempealeau-Jackson County line to Black River Falls Dam (miles 37.01 to 73.36) was put on the Impaired Waters List in the 1998 cycle for Mercury and PCBs in fish tissue. The Mercury listing was removed in 2008. In the 2018 cycle this water was also listed for elevated phosphorus. Evaluation in the 2022 cycle found fish communities in excellent condition.

Black River from Black River Falls dam to Lake Arbutus dam (miles 73.36 to 86.9) was put on the Impaired Waters List in the 1998 cycle for mercury in fish tissue. This river segment was evaluated in the 2012, 2018, and 2022 cycles; phosphorus levels were too high, but chloride levels were low, and bug and fish communities were in good condition.

Black River from Lake Arbutus inlet to Cunningham Creek (miles 89.75 to 99.17) was put on the Impaired Waters List in the 1998 cycle for mercury in fish tissue. Phosphorus was added to the list in the 2014 cycle. Evaluation in the 2020 and 2022 cycles showed bug and fish communities in good condition.

Black River from Cunningham Creek to Grand Ave. in Neillsville (miles 99.17 to 103.21) was put on the impaired waters list for mercury in fish tissue. Phosphorus impairment was added to the list in 2014.
Black River from Grand Ave, Neillsville, to HWY H (miles 103.21 to 110.83) was put on the impaired waters list for phosphorus in 2018.

Black River from Hwy H to Rock Creek (miles 110.83 to 119.8) was put on the impaired waters list in 1998 for low dissolved oxygen and mercury in fish tissue. Phosphorus impairment was added to the list in 2018.

Black River from Rock Creek to Hwy 29 (miles 119.8 to 136.96) was put on the impaired waters list for phosphorus in 2018.

Black River from Hwy 29 bridge to the Clark/Taylor county line (miles 136.96 to 145.24) was put on the impaired waters list for phosphorus in 2018.

Black River from Taylor/Chippewa county line to Medford Flowage (miles 145.24 to 180.98) was put on the Impaired Waters List for mercury during the 1998 cycle. Evaluation every two-year cycle from 2016 to 2022; phosphorus levels were elevated and also added to the list.

Black River from Medford Flowage inlet to CTH M (miles 181.41 to 187.94) was evaluated for phosphorus and biology every two-year cycle from 2018 to 2022; phosphorus was consistently elevated and put on the Impaired Waters List in the 2022 cycle.

Black River from CTH M to headwaters (miles 187.94 to 203.42) was evaluated every two-year cycle from 2016 to 2022; bug and fish data indicated good conditions, but in the 2022 cycle phosphorus levels were too high. This river segment is proposed for the 2022 Impaired Waters List.

Date  2022

Author  Ashley Beranek


Wisconsin has over 84,000 miles of streams, 15,000 lakes and milllions of acres of wetlands. Assessing the condition of this vast amount of water is challenging. The state's water monitoring program uses a media-based, cross-program approach to analyze water condition. An updated monitoring strategy (2015-2020) is now available. Compliance with Clean Water Act fishable, swimmable standards are located in the Executive Summary of Water Condition in 2018. See also the 'monitoring and projects' tab.



Citizen-Based Stream Monitoring
Collect chemical, physical, and/or biological water quality data to assess the current overall stream health. The data can inform management decisions and may be used to identify impaired waters for biennial lists.
Monitor or Propose 303(d) Listing
Chemistry samples for total phosphorus and Chlorophyll a will be collected in Lake Arbutus to determine if current in-lake conditions meet water quality standards and to verify, per WisCALM guidance, whether 303(d) listing is appropriate for this lake. This project will fund the first of two years of sampling.
Monitor Water Quality or Sediment
Category 3. 2018 TP Results: May Exceed. Station: 613086. AU: 201404.
Rivers Management Grant
The Friends of the Black River proposes to continue funding its program development specialist position to coordinate new and existing FBR programs including: 1) water quality testing, 2) native and invasive species identification, 3) maintenance of local access sites, 4) river clean-up events, 5) new member recruitment, 6) strategic planning, 7) organizational leadership training.
Partnership Project
Friends of the Black River proposes to hire a Program Development Specialist to coordinate a public Conservation Forum for the purpose of identifying partner organizations and recruiting volunteers, and to lay the groundwork for and organize future studies, activities and events to enhance understanding and protection of the Black River ecosystem. FBR will also pursue organizational development and leadership training through the Wisconsin River Alliance.
Engage Volunteers in Monitoring/Restoration
The Taylor County Land Conservation Department will lead an effort to educate the public on water resources, establish a citizen based stream monitoring network, conduct stream monitoring, and organize a county wide waterway association. Specific activities will be to: * Develop partner organization to support and complete the project. * Establish citizen based stream monitoring program and conduct monitoring. * Conduct educational and monitoring training for interested participants. * Advocate for the formation of new local river organizations in Taylor County. Specific products or deliverables will include: * Stream monitoring data and GIS maps of monitoring locations. * Published results of the education and monitoring activities. * A final public informational meeting to encourage continuation of river protection activities.
Partnership Project
Jackson County proposes to sponsor, in cooperation with the DNR Black-Buffalo-Trempealeau Basin Partnership Team, an effort to further develop an organization for preservation, conservation and education associated with the Black River basin, and to establish a strategic plan. Major elements of the project to include: 1) hire an executive director, 2) organize and conduct a river clean-up event, 3) production of education and outreach materials, 4) conduct workshops toward development of a strategic plan, 5) final report. Educational materials will be made available to the public through canoe rental shops, the camper of commerce, mailings and through meetings, workshops and other events. The strategic plan will be presented to local land use decision makers and DNR staff.
Partnership Project
Jackson County, in coordination with the DNR's Black-Buffalo-Trempealeau (BBT) Basin Partnership Team, proposes to sponsor the start-up of an organization focused on preservation, conservation and education regarding the Black River basin. Key project elements to include: 1) hiring of an executive director, 2) generation of public interest through river clean-up event, 3) workshops, 4) development, use and distribution of newsletters, a brochure, powerpoint presentation and other publicity materials, 5) development and distribution of a final report. Information produced and publicity regarding events will be shared with the UW-Extension Water Action Volunteer network and with the public through workshops, articles and mailings.
Water Quality Planning
The BR03 watershed contains six HUC 12 watersheds. The six HUC 12 watersheds to be assessed in this project include Rathbone-Soper, Spencer-Big, Roaring-Black, Douglas, Davis-Black and Sand. Of these six watersheds, two were identified for Targeted Watershed Assessment (TWA). The Sand Creek HUC 12 watershed was identified as healthy but threatened designated for protection. The Rathbone and Soper Creeks HUC 12 watershed was identified for evaluation due to stressed biological surveys. The Rathbone - Soper HUC 12 watershed was selected as one of the TWA’s for the Western District to monitor in the 2014 field season
Monitor Water Quality or Sediment
The lower 90% CI is 75.869. This is barely over the standard. The next 2 sites US in the next AU, near Chelsea, the TP are not that high. Those were DNR and looks like DNR and Taylor Co samples. These new samples are collected by Taylor Co, I think the data is probably OK as I look at their other sites and after talking to the LCD, but with lower TP values just US in a different AU and the lower CI so close to 75. I am not sure if these values are reflective of this AU. I?m cautious about listing a stream so close to the standard. We should hold off listing for this cycle and see if Taylor Co continues to sample and see if the values stay high.
Runoff Evaluation
DNR Water Division staff should assess nonpoint sources and other potential sources which appear to have caused a decline in the trout population in the Black River above Medford.
Monitoring Ecosystem
A comprehensive mussel survey should be conducted on the Black River and its major tributaries.  Before any decision is made to riprap eroding sand banks of the Black River, a mussel survey should be conducted.
Lakes Planning Grant
The following lakes should be considered high priorities for a lakes planning grant for developing lake management alternatives:  Black River Flowage  Wazee Lake  Oakwood Lake  Trow Lake  Lake Arbutus  Snyder Lake  Sportsman Lake  Diamond Lake  Hulls Lake  Richter Lake  Clear Lake  Esadore Lake  Sackett Lake  Bugle Lake  Crystal Lake  Lake Henry  Martha Lake  Mirror Lake
Monitor Fish Tissue
1676700 name Black R. (Below Medford) TMDL ID 582 Start Mile 132.67 End Mile 168.4
Monitor Fish Tissue
1676700 name Black River TMDL ID 51 Start Mile 77.18 End Mile 90.64
Monitor Fish Tissue
1676700 name Black River TMDL ID 2012-56, 51, 707 Start Mile 0 End Mile 24.44
Monitor Fish Tissue
1676700 name Black River, Hwy H To Rock Creek TMDL ID 50 Start Mile 98.14 End Mile 107.12
Wastewater Monitoring or Management
The Town of Onalaska, the Onalaska Lake District, and major industries in the Brice Prairie area should re-examine sewering all or portions of the Brice Prairie.
Wastewater Monitoring or Management
Water Division staff should work with the Black River Correctional Center to determine if an upgrade or a new wastewater treatment facility is needed. (Type B)
Monitor to Evaluate Projects
Water Division staff should conduct fishery surveys on streams in the Lower Black River watershed to document fish community changes since implementation of best management practices. (Type B)

Standards Details

This water, from Medford to CTH M, is a Class III Trout Stream, and from CTH M to the headwaters it is a Class II Troutwater.

Date  1980

Author   Aquatic Biologist

Management Goals

Wisconsin's Water Quality Standards provide qualitative and quantitative goals for waters that are protective of Fishable, Swimmable conditions [Learn more]. Waters that do not meet water quality standards are considered impaired and restoration actions are planned and carried out until the water is once again fishable and swimmable

Management goals can include creation or implementation of a Total Maximum Daily Load analysis, a Nine Key Element Plan, or other restoration work, education and outreach and more. If specific recommendations exist for this water, they will be displayed below online.


Monitoring the condition of a river, stream, or lake includes gathering physical, chemical, biological, and habitat data. Comprehensive studies often gather all these parameters in great detail, while lighter assessment events will involve sampling physical, chemical and biological data such as macroinvertebrates. Aquatic macroinvertebrates and fish communities integrate watershed or catchment condition, providing great insight into overall ecosystem health. Chemical and habitat parameters tell researchers more about human induced problems including contaminated runoff, point source dischargers, or habitat issues that foster or limit the potential of aquatic communities to thrive in a given area. Wisconsin's Water Monitoring Strategy was recenty updated.

Grants and Management Projects

Monitoring Projects

Watershed Characteristics

Black River is located in the O'Neill and Cunningham Creeks watershed which is 161.85 mi². Land use in the watershed is primarily agricultural (39.90%), forest (31.20%) and a mix of grassland (16%) and other uses (12.90%). This watershed has 329.34 stream miles, 86.59 lake acres and 9,581.29 wetland acres.

Nonpoint Source Characteristics

This watershed is ranked Not Ranked for runoff impacts on streams, Not Available for runoff impacts on lakes and High for runoff impacts on groundwater and therefore has an overall rank of High. This value can be used in ranking the watershed or individual waterbodies for grant funding under state and county programs.However, all waters are affected by diffuse pollutant sources regardless of initial water quality. Applications for specific runoff projects under state or county grant programs may be pursued. For more information, go to surface water program grants.

Natural Community

Black River is considered a Warm Mainstem, Cool-Cold Mainstem under the state's Natural Community Determinations.

Natural communities (stream and lake natural communities) represent model results and DNR staff valiation processes that confirm or update predicted conditions based on flow and temperature modeling from historic and current landscape features and related variables. Predicated flow and temperatures for waters are associated predicated fish assemblages (communities). Biologists evaluate the model results against current survey data to determine if the modeled results are corect and whether biological indicators show water quaity degradation. This analysis is a core component of the state's resource management framework. Wisconsin's Riverine Natural Communities.

Warm Mainstem waters are moderate-to-large but still wadeable perennial streams with relatively warm summer temperatures. Coldwater fishes are absent, transitional fishes are common to uncommon, and warm water fishes are abundant to common. Headwater species are common to absent, mainstem species are abundant to common, and river species are common to absent.

Cool (Cold-Transition) Mainstem streams are moderate-to-large but still wadeable perennial streams with cold to cool summer temperatures. Coldwater fishes are common to uncommon, transitional fishes are abundant to common, and warm water fishes are uncommon to absent. Headwater species are common to absent, mainstem species are abundant to common, and river species are common to absent.