Overview

The main stem of the Manitowoc River, formed by the confluence of the North and South branches of the
Manitowoc River, flows eastwardly approximately 36 miles before entering Lake Michigan at the city of
Manitowoc. The river has two distinct portions: The upper half, above Clarks Mills, is wide, sluggish, and
marshy with a soft bottom and a gradient of about one foot per mile; below Clark Mills, the gradient
increases to about 12 feet per mile, the river becoming shallow and fast, with a bottom composed
primarily of rock in sizes from gravel to boulder, with an occasional sand bar. The steep gradient
continues 16.4 miles downstream to the Manitowoc Rapids where 4.8 miles upstream from Lake
Michigan the river slows as it approaches lake level. This lower stretch of river has deep natural pools and
dredged areas (Peeters 1990). The overall water quality, based on the Hilsenhoff Biotic Index, was good
(1990) at the two stations monitored below the Clarks Mills Dam. The stream habitat evaluation at these
same sites were fair to good (1990). One site was also monitored above the Clarks Mills Dam. The biotic
index rated the stream as fair and the stream habitat as good (WDNR 1995). Additional monitoring will
be conducted on the Manitowoc River as part of the basin long-term water quality trend assessment. Refer
to the recommendations report for more information.
Historic reductions in the percentage of forested and wetland vegetation have resulted in a watershed that
lacks adequate opportunities for infiltration and retention of precipitation and snow melt resulting in
flashy runoff which overwhelms existing stream channels and aquatic habitat. This excessive runoff also
strips valuable sediments and nutrients from the terrestrial environment and delivers them to our streams
and lakes where they result in degraded water quality and poorer habitat which can kill sensitive and
intolerant fish and aquatic invertebrates. Flashy runoff also limits the amount of water available to
sustain adequate flows during drought. Restoration efforts should focus on increasing the overall
percentage of forested and wetland vegetation in this watershed to restore a more natural hydrologic
regime and minimize the impacts of flashy runoff and an altered hydrologic regime.
Most of the land use along the river is agricultural. The upper reaches are extensive river bottoms that are
difficult, if not impossible, to farm in some locations. These wet soils are conducive to erosion and
runoff; the lower reach of the river flows through Manitowoc. There are nearly 150 acres of adjoining
wetlands in the vicinity to the west of the Collins Marsh area. The wide-open, non-wooded stretch of river
10 miles upstream of Clarks Mills is a wildlife area of concern.
Beginning in the 1960s and continuing into the 1980s, the area of the Manitowoc River below the dam at
Manitowoc Rapids was managed as part of the Lake Michigan trout and salmon program. When the trout
and salmon program began in the 1960s, hatchery trucks simply delivered trout and salmon to Lake
Michigan harbors. Trout and salmon stocking programs have changed throughout the years with modified
fish management techniques. Tiger trout are no longer stocked; coho salmon stockings were moved to the
south end of Lake Michigan, and lake trout stockings were moved to reefs in protected refuges.
In the 1970s and early 1980s, snagging of fish was allowed in rivers where salmon had been stocked and
were returning as mature adults on a dead end spawning run. As part of this policy, chinook salmon were
stocked and snagging was permitted in the Manitowoc River.

From: Willman, Guy and Mike Toneys. 2001. The State of the Lakeshore Basin. Wisconsin Department of Natural Resources, Madison, WI.

Date  2001

Author  Michael Toneys

Overview

In the early 1980's, an internal WDNR steelhead trout committee worked to improve a faltering rainbow trout program, placing emphasis on stocking improved steelhead strains of rainbow trout in select rivers to improve the recreational fishery. Snagging was not compatible with this program, which established guidelines precluding steelhead stocking in rivers where snagging was allowed.
In 1983, the dam on the Manitowoc River at Manitowoc Rapids was removed. In preparation for developing a steelhead trout project on the Manitowoc River, chinook salmon stocking was moved away from the river in 1983, and in 1984, the snagging season was discontinued in the Manitowoc River. The Manitowoc River is one of the Lake Michigan tributaries managed by WDNR as a Class I steelhead stream and as such receives annual smolt stockings of the chambers creek, ganaraska and skamania strains of steelhead. The river also receives stocking of brook trout, brown trout, chinook and coho salmon.
In 1944, the Oslo dam on the Manitowoc River upstream of North Union Road was abandoned. A section of the dam failed in the 1960's, and in 1985, the dam was breached and much of the material was removed from the stream to allow upstream migration of fish. Finally the dam was removed in the early 1990's. The Manitowoc Fish and Game Club developed the site as a public angler access area (Surendonk 1996).
Fish management of the Manitowoc-Branch River system changed significantly in the spring of 1986 when, as part of the larger steelhead trout study, anadromous strain steelhead were stocked in the Branch River. From 1986 through 1988, more than 430,000 steelhead smolt were stocked in the Branch River. These steelhead smolt were released in an upriver area to improve imprinting and subsequent homing by adults to the Manitowoc-Branch River system. Fall fingerling coho were also stocked into the Manitowoc River system in 1988. This representsed the first plant of coho in the Manitowoc River in more than a decade. Ongoing steelhead syurveys will facilitate evaluations of this coho plant. A WDNR Lake Michigan Steelhead Management Plan calls for continued steelhead sotcking in the Manitowoc-Branch River system. Currently, Fisheries staff stock chinook and coho salmon, brown trout, brook trout, and two strains of steelhead in the Manitowoc River.
A U.S. Geological Survey gaging station is located on the Manitowoc River on the right bank 300 fett upstream from the County Trunk Highway JJ bridge, just west of the Manitowoc sity limits and 6.6 miles upstream of the mouth. Discharge data has been collected since July 1972.

From: Willman, Guy and Mike Toneys. 2001. The State of the Lakeshore Basin. Wisconsin Department of Natural Resources, Madison, WI.

Date  2001

Author  Michael Toneys

Impaired Waters

Manitowoc River from its mouth to Revere Street bridge (miles 0 to 2.02) was put on the impaired waters list in 2002 for PCBs and PAHs in sediment and PCBs in fish tissue. Evaluation of bug communities in the 2022 cycle showed them in good condition.
Manitowoc River from Revere Street in Manitowoc to Clarks Mills dam (miles 2.03 to 20.74) was put on the impaired waters list in 2002 for PCB contaminated sediment and fish tissue. A listing for phosphorus and degraded biology was added in 2012. This segment was evaluated every two-year cycle from 2012 to 2022; phosphorus was consistently elevated.

Manitowoc River from Clarks Mills dam to confluence of the North and South branches (miles 20.74 to 35.81) was put on the impaired waters list in 1998 for PCB contaminated sediment and fish tissue. Assessments of new data during the 2020 listing cycle showed temperature levels appropriate for healthy aquatic communities like plants, fish, and bugs; available fish and bug sample data were in good condition.

Date  2022

Author  Ashley Beranek

Condition

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.

Reports

Recommendations

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

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

Manitowoc River is located in the Lower Manitowoc River watershed which is 168.33 mi². Land use in the watershed is primarily agricultural (47%), wetland (19.50%) and a mix of grassland (17.90%) and other uses (15.50%). This watershed has 264.70 stream miles, 2,910.36 lake acres and 19,995.06 wetland acres.

Nonpoint Source Characteristics

This watershed is ranked High for runoff impacts on streams, Not Ranked 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.