The Menomonee River watershed is
approximately 135 square miles and covers
much of the southern portion of the
Milwaukee River basin. The watershed spans
four counties and more than a dozen
municipalities. As part of the Milwaukee metro
area, the land use is predominantly urban and
suburban, especially in the watershed's
southern half. The Menomonee River
watershed has over 75 miles of streams and
rivers, many of which are impaired.

Impairments for aquatic toxicity are common,
with phosphorus, sediment, and bacteria
frequently cited as pollutants of concern.

Given the highly urbanized nature of the
watershed, efforts to restore the Menomonee
River have focused on point sources. In
particular, municipal separate storm sewer
systems (MS4s) were identified as a primary
source of pollutants. In 2011, watershed
partners (collectively, the Menomonee River
Watershed Permittees) united to develop a
framework for a watershed -based approach
that would address discharges from their MS4.

Wisconsin Department of Natural Resources
(DNR) then incorporated the framework into a
watershed-based MS4 permit in 2012 and
renewed in 2020. The permit takes advantage of opportunities to collaborate, while still requiring
specific activities from each municipality to protect and restore water quality in the watershed.

This case study examines the 2020 multisource watershed-based permit, Wisconsin Pollutant
Discharge Elimination System (WPDES) Permit No. WI-S065404-2, which is the renewal of the original

v^EPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin


Menomonee River Watershed, Wisconsin
Key Water Quality Concerns

Total phosphorus, total suspended solids, fecal coliform, and

Stakeholder Involvement Techniques

•	Workgroup meetings to develop watershed-based
permit framework.

•	Permit requirements for public comment for annual
reports, Storm Water Management Plan revisions,
adoption of ordinances, and Total Maximum Daily Load
reduction benchmark development.

•	Permit requirements for public education and outreach

Case Study Issues of Interest
Type of Point Sources


H I; Municipal Separate Storm Sewer System Discharges
Type of Watershed-Based Permit or Approach

Multisource Watershed-Based Permit
Highlighted Approach(es)

# Implementation of Total Maximum Daily Loads
(TMDLs) or Other Watershed Pollutant Reduction

watershed permit. The permit implements the 2018 Milwaukee River total maximum daily loads


As noted above, the Menomonee River
watershed is heavily urbanized. Like many urban
watersheds, the water bodies are impaired due
to a variety of issues. Impairments for aquatic
toxicity (both acute and chronic) are common, as
are impairments to recreation and for degraded
biological communities. Water quality studies
indicated that phosphorus is a primary cause.

Bacteria (typically fecal coliform or £ colt) is also
linked to impairments, while sediment (through
erosion and sedimentation) is a vector for
transporting phosphorus and degrades habitat.

Chloride is another commonly identified
pollutant; the impacts of using salts and deicers
for winter road management is a growing
concern for many water bodies.

The approach for addressing MS4 discharges in the Menomonee River has evolved over the last
decade. Prior to 2011, eight of the municipalities in the Menomonee River watershed held a joint MS4
permit that covered their political boundaries (i.e., not the watershed boundaries). Many other
municipalities in the watershed had their own MS4 permit. Using the joint MS4 permit as a starting
point and informed by the parallel development of TMDLs to address impairments in the Milwaukee
River basin, the Milwaukee Metropolitan Sewerage District (MMSD) convened a workgroup and
developed a framework for a watershed-based permit to address urban stormwater discharges in the
watershed. Using the framework, DNR issued the Menomonee River Watershed MS4 Permit in 2012.
DNR and MMSD finalized development of phosphorus, sediment, and bacteria TMDLs for the
Milwaukee River in 2018. The permit was revised in 2020 to incorporate the applicable TMDL
wasteload allocations.

Permit Strategy

In 2011, MMSD was awarded a grant from EPA to develop the framework for a watershed-based MS4
permit for the Menomonee River watershed. Through a collaborative, stakeholder-driven process,
localities in the watershed—along with MMSD, DNR, the Southeastern Wisconsin Regional Planning
Commission (SEWRPC), and several non-governmental organizations—formed a workgroup to
develop a framework for the watershed-based permit.

The workgroup developed this framework using the principles of several recent efforts in the
watershed, including an update to the regional water quality management plan, a vision plan for
MMSD's facilities, and a watershed restoration plan. These documents provided recommendations for
watershed improvements that were incorporated into specific permit conditions that could be applied
at the watershed scale. The workgroup also utilized EPA's August 2007 Watershed-based National
Pollutant Discharge Elimination System (NPDES) Permitting Technical Guidance. Lastly, the TMDLs for
the Milwaukee River were also under development at this time, and the workgroup considered
information from that process as it became available.

The TMDLs were developed for the Milwaukee River
basin, which includes the Menomonee River
watershed. DNR typically manages TMDL
development, but in this case, several watershed
partners had already assembled water quality data and
developed watershed models. MMSD and the
Southeastern Wisconsin Regional Planning
Commission led a team in developing a "third-party"
TMDL supported by grant funding from EPA. This
TMDL identified the primary sources of phosphorus,
sediment, and bacteria and established wasteload
allocations for permitted sources, which DNR then
incorporated into WPDES permits. While the TMDLs
recognized that implementation and demonstrating
compliance could be accomplished on a more
collaborative basis, group or watershed-based permits
assigned individual wasteload allocations for
municipal permittees.

oEPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

The workgroup met numerous times during this process. Smaller groups also met periodically to
preview certain topics for the larger workgroup, such as the details of the watershed-based permit or
education and outreach issues. Several questions proved to be driving factors in the discussions, such

•	Is a watershed-based approach better than the current permitting approach?

•	How can the permit be structured to include communities that are in more than one watershed?

•	What are the economic benefits to municipalities?

•	Can water quality trading be included in the permit?1

Next, the workgroup studied water quality data for the Menomonee River watershed. Consistent with
the ongoing TMDLs, phosphorus and bacteria were found to frequently exceed the water quality
standards. The data for suspended sediment were less conclusive; mean concentrations of total
suspended solids were generally fairly low. But the results varied considerably for individual samples,
with some as high as two orders of magnitude larger than the average concentration. Given the
relationship of sediment to other pollutants, and the presence of several sediment impairments,
suspended sediment remained a pollutant of concern.

Over the course of nearly a dozen meetings, the workgroup developed an annotated draft of a
watershed-based permit and fact sheet for DNR, as well as an informational sheet for elected officials,
a list of incentives for MS4s to participate in the permit, and other materials. The resulting final permit
from DNR encourages the localities to identify common goals and share resources, while still working
to make progress within each individual municipality. The workgroup had also conducted significant
outreach to MS4s in the watershed; 11 of the possible 18 localities were interested in participating,
covering nearly 90 percent of the watershed area.2 Perhaps most importantly, the workgroup achieved
consensus on the approach. By soliciting and including the needs of the participating municipalities,
the chances of success for the watershed-based permit greatly increase.

DNR issued the first watershed-based permit in 2012. In 2018, DNR and MMSD finalized the
Milwaukee River TMDLs, which included wasteload allocations for phosphorus, sediment, and bacteria.
In 2020, DNR renewed the watershed-based permit and incorporated the pollutant reductions needed
to meet the 2018 TMDLs into the permit.

Permit Components

The permit has two categories of requirements: individual and shared. Individual responsibilities are
those that apply to a specific municipality. Some individual responsibilities apply to all permittees,
while others are targeted to one or more individual permittees. Shared responsibilities are permit
conditions that the municipalities may work collaboratively to fulfill.

The following are examples of individual responsibilities included in the permit:

•	"The permittee shall have a written stormwater management program (SWMP) that describes in
detail how the permittee intends to comply with the permit requirements for each minimum
control measure." (Permit Section II)

1	See Development of a Framework for a Watershed-Based Municipal Stormwater Permit for the Menomonee River watershed
(SEWRPC 2013, p. 7) for more detailed information about how these questions were discussed and resolved within the

2	The localities that did not participate had relatively small land areas and were already members of other watershed permit

oEPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

•	Each MS4, excluding Milwaukee County, must by September 30, 2021 "[c]onduct a survey or use
other appropriate methods to identify their education needs...[and] [s]ubmit a list of prioritized
storm water education needs for their community including the methods and rationale used for
prioritization." By September 30, 2023, each permittee must "provide education and outreach
within the MS4 boundary for at least one prioritized education topic[,] [d]evelop metrics that will
be used for measuring progress after the education event has been held[, and] [s]ubmit as part
of the permit application (due September 30, 2024), a summary of the results of the education
efforts and planned targeted education for the next permit term." (Permit Section II.B)

•	"The Village of Butler shall: Complete at least two water quantity or quality projects."

(Permit Section III.B.2.a)

•	"The City of Greenfield shall: Update the City's stormwater website to provide additional
educational material and promote usage of rain barrels." (Permit Section III.B.5.a)

•	"The City of West Allis shall:... Develop and implement a green infrastructure plan for City
parking lots. The City shall implement green infrastructure on three lots during the permit term."
(Permit Section III.B.9.b)

The following are examples of shared responsibilities and opportunities for cooperation included in
the permit:

•	"The Menomonee River Watershed Permittees shall implement a written public education and
outreach program to increase the awareness of how the combined actions of human behavior
influence stormwater pollution and its effects on the environment." (Permit Section 11. A)

•	"The Menomonee River Watershed Permittees' implementation of one or more of the conditions
of this permit may incorporate cooperative efforts with other MS4 regulated permittees or
efforts by other groups or organizations if the shared responsibility is approved by the
Department." (Permit Section I.D.2)

•	"Where appropriate, completion of a benchmark may incorporate cooperative efforts with other
entities regulated or not by this permit on the condition that requirements defined in section
I.D.2. of this permit are upheld." (Permit Section III.B)

By including both types of requirements, the permit accomplishes the dual goals of leveraging
common tasks and pooling resources while still maintaining enough specificity to achieve individual
goals within each community. Permittees have opportunities to collaborate, while ensuring that
pollution reductions are equitable and progress is being made in all parts of the watershed. The
structure of the permit also provides an opportunity for permittees to assist others in their individual
efforts. For example, when required to address fecal coliform loading within their individual
municipality, individual permittees worked together to share their knowledge, experiences, challenges,
and advice, which helped each permittee implement practices within their own municipality.

Collaborative Education and Outreach Programs

A significant shared responsibility within the permit is to develop and implement a public education
and outreach program, with an emphasis on how human behavior affects stormwater. The outreach
program must address nine topics:

•	Illicit Discharge Detection and Elimination

•	Household Hazardous Waste Disposal/Pet Waste Management/Vehicle Washing

•	Yard Waste Management/Pesticide and Fertilizer Application

•	Stream and Shoreline Management

•	Residential Infiltration

•	Construction Sites and Post-Construction Storm Water Management

oEPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

•	Pollution Prevention

•	Green Infrastructure/Low Impact Development

•	Snow and Ice Control

For each topic, the outreach program must identify the pollutants of concern, the target audience, and
other key information. All the topics must be addressed at least once in the permit term, and at least
three topics must be addressed each year.

To facilitate the education and outreach program,
the municipalities have partnered with the non-
government organization Southeastern Wisconsin
Watersheds Trust, which created the Respect Our
Waters campaign. The campaign is multifaceted
and has tips for homeowners and businesses for
reducing stormwater pollution. The campaign
website provides general watershed-level
educational material and specific how-to videos
for certain best management practices (BMPs). It
also serves as a hub for the MS4 communities by
posting information on reporting, links to training
courses, and providing flyers for public events.

The municipalities are encouraged to further develop programs unique to their individual jurisdiction
and to work with municipalities that are not Menomonee River watershed permittees.

TMDL Load Reductions

To meet the load reductions in the TMDLs, each municipality is required to complete several analyses.
These include:

•	A pair of reports (due midway through the
permit term) that include a detailed map of
the MS4 area, analyses of pollutant loadings
for each subwatershed, a summary of all
structural and nonstructural BMPs, a
description of the methodology for
measuring progress toward meeting the
TMDL requirements, and other information.

•	A document updating the pollution
reduction benchmarks (see text box) for
phosphorus and sediment when BMP
implementation is not achieving the needed

•	An inventory of suspected sources of fecal
coliform entering the MS4, as identified by
the illicit discharge program. The
municipality must subsequently develop a
plan to eliminate sources of bacteria,
including prioritizing activities, proposed
BMPs, projected costs, and a proposed schedule.

Individual Outreach Requirements

In addition to the collaborative education and
outreach activities, each municipality must also
implement targeted outreach within their own
jurisdiction. Each MS4 must conduct a survey or other
mechanism to identify and prioritize local needs for
stormwater education. The municipality is then
required to address at least one of these priority
topics within the permit term. Each municipality must
submit documentation of this effort, including
metrics on measuring progress and plans for
subsequent educational efforts, as part of its next
permit renewal application.


The TMDLs called for significant reductions in
sediment and nutrient loading. In many
subwatersheds, the percent reduction needed to
restore water quality was over 70 percent. To allow
municipalities enough time to develop a strategy to
achieve those reductions, while also demonstrating
"reasonable assurance" that the TMDLs are being
implemented, DNR and the permittees developed
the idea of benchmarks. DNR asked each
municipality to identify specific activities, or
benchmarks, that they would complete within the
permit term. (Note that some of these benchmarks
are the same activities listed above as individual
responsibilities.) Each municipality must also update
their benchmarks for phosphorus and sediment, as
well as bacteria, prior to the next permit renewal. This
iterative approach incorporates the concepts of
adaptive management, an important addition for a
long-term project.

oEPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

As noted above, each municipality also has individual requirements specific to their MS4. Examples
include completing specific BMPs (many are already identified in the municipalities' planning
documents), developing maintenance programs, performing studies to inform future decisions, and
conducting outreach and education activities.

Post-Construction Stormwater Management

In addition to standard language to develop and implement a post-construction stormwater program
(including an ordinance, adherence to state design criteria, plan reviews, and more), the permit has
two additional requirements:

•	Develop a system to track the installation and maintenance of all post-construction BMPs,
whether on public or private land. The system will ensure that long-term maintenance is
performed, allowing the BMPs to continue to be credited toward meeting the load reductions of
the TMDLs.

•	Review existing ordinances for construction, design, landscaping, and other related topics to
identify barriers to the implementation of green infrastructure within the MS4 area. Once
barriers have been identified, each municipality is required to revise their ordinance accordingly.
Removing barriers will provide developers and landowners with more options to comply with
post-construction requirements.

Winter Road Management

Each municipality is required to develop a winter roads management program. The use of road salts
has been linked to elevated chloride levels in many watersheds and is a growing concern for aquatic
life, as well as public health. Drinking water authorities monitor sodium levels out of concern for
cardiac patients. Salt removal is also expensive, especially at the scale of an entire drinking water
facility. But public safety is also a paramount concern—keeping the roads safe during the winter is
critical to driver safety and keeping the local economy moving. Protecting water quality while also
ensuring public safety is a complex balancing act for managers. Therefore, winter road management
in the Menomonee River watershed involves the use of BMPs, such as calibrating application
equipment, tracking salt usage, and educating the public on sound use of salts and deicers.

Permit Effectiveness
Environmental Benefits

Although it is too early to tell if the watershed-based permit has improved water quality, DNR
anticipates that implementing the permit will help achieve the TMDL wasteload allocations and
attainment of water quality standards in the watershed.

Benefits to the Permittee

The workgroup identified a number of benefits to participating in the watershed-based permit,

•	Collaborative watershed projects that could meet multiple goals.

•	Improved targeting of illicit discharges.

•	Cooperative public outreach efforts.

•	Joint annual reporting.

•	Ability to address water quality without limitations inherent in trading.

•	Improved priority ranking for grant applications.

EPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

The initial workgroup identified potential challenges associated with a watershed-based approach,
including accounting for MS4s located in more than one watershed, implementing the six minimum
measures required for regulated small MS4s in a large group permit, and overcoming political hurdles,
as well as possible statutory changes required for this approach. The workgroup also needed to figure
out how to write specific permit conditions in situations requiring collaboration and joint compliance.

Most of the anticipated challenges identified by the initial workgroup were not significant barriers to
implementation. However, some individual permittees experienced political hurdles when evaluating
collaborative efforts because of the perception that they would be spending funds to address
stormwater outside their individual jurisdiction. Unfortunately, many of these hurdles were perceived
to be too large to overcome. As collaboration continues to be fostered through this group structure
and potential projects must be evaluated for permit compliance, it may be possible to overcome these
hurdles in the future.

The watershed-based permit has resulted in increased collaboration between permittees. The level of
collaboration among this group of permittees is unique and a key benefit of the watershed-based
permitting approach. In addition to working together on compliance activities, the permittees meet
periodically to discuss how things are going, the challenges they are facing, and what strategies are
working. They also share implementation information (e.g., monitoring for bacteria) and their
experiences working with consultants.

Benefits to the Permitting Authority

The watershed-based permit has led to efficiencies for DNR in permitting, compliance determinations,
and providing assistance to permittees. For example, DNR staff are able to talk to the group of
permittees about permitting issues at the same time, rather than individually. DNR can also review
annual reports and other submissions required by the permit concurrently.

The permit has also led to improvements in TMDL implementation. It was the first permit in the state
to incorporate TMDL wasteload allocations for bacteria. The permittees shared their implementation
challenges and suggestions for improving the permit conditions with DNR staff. Using this
information, DNR modified the conditions in subsequent permits issued to other permittees subject to
the TMDL.

Lessons Learned

Samantha Katt of DNR shared her lessons learned from developing and implementing the watershed-
based permit.

According to Ms. Katt, one of the challenges of developing the watershed-based permit was writing
permit conditions (e.g., outfall screening, illicit discharge detection and elimination, bacteria TMDL
implementation projects) that are appropriate for 13 municipalities with varying sizes, landscapes
(rural, suburban, and urban), and resources. In developing the permit conditions, DNR strived to
achieve fairness among permittees, while also recognizing that the requirements necessary for each
permittee to reduce pollutants in the discharge from their systems to the "maximum extent
practicable"3 would vary.

3 The federal regulations require that permits for discharges from small MS4s include requirements to reduce pollutants in
discharges to the maximum extent practicable to protect water quality and satisfy the Clean Water Act's water quality
requirements. (40 CFR 122.34(a))

oEPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

With such a large group of permittees, she also found it challenging to ensure all permittees
understood the permit conditions, especially those related to the bacteria TMDL. While DNR held
meetings with the full group of permittees, it also met with individual permittees to ensure their
understanding. The individual meetings also provided an opportunity for permittees to voice concerns
they did not feel comfortable sharing in the large group setting.

Ms. Katt believes the watershed-based permitting approach used in the Menomonee River watershed
could be applied in other watersheds. Wisconsin DNR has developed similar watershed-based permits
for MS4 permittees, including:

•	WPDES Permit No. WI-S058416, which provides coverage for 22 permittees comprising the
Madison Area Municipal Stormwater Partnership.

•	WPDES Permit No. WI-S061557, which provides coverage for the city of Mequon and village of

•	WPDES Permit No. WI-S061565, which provides coverage for seven permittees comprising the
North Shore Group.

DNR is considering encouraging other MS4 permittees to apply for watershed-based permits, which
could provide for enhanced collaboration opportunities and efficient use of resources.

EPA Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin


Hahn, M. SEWRPC. February 27, 2014. Watersheds Know No Political Boundaries: A Look into the
Benefits and Challenges of Watershed-BasedStormwater Permitting in Southeastern Wisconsin. 2014
Government Affairs Seminar, http://cswea.org/wp-content/uploads/2017/09/1Q15-
WBP pres to 2014 Wis Govt Affairs Seminar 00216265 Michaei Hahn.pdf.

SEWRPC. November 2007. Water Quality Conditions and Sources of Pollution in the Greater
Milwaukee Watersheds. http://www.sewrpc.org/SEWRPCFiles/Publications/TechRep/tr-039-part-01-

SEWRPC. January 2013. Development of a Framework for a Watershed-Based Municipal Stormwater
Permit for the Menomonee River Watershed. Memorandum Report No. 204.

SEWRPC. A Regional Water Quality Management Plan Update for the Greater Milwaukee Watersheds.
Amended May 2013. http://www.sewrpc.org/SEWRPCFiies/Pubiications/pr/pr-050 part-
1 water quaiitv pian for greater mke watersheds.pdf.

Southeastern Wisconsin Watershed Trust. Respect Our Waters.

Southeastern Wisconsin Watershed Trust. Aprii 28, 2020. Menomonee Watershed Permit Adopted
[Press Release], https://www.swwtwater.org/news/2020/4/20/menomonee-watershed-permit-

EPA. December 2003. Watershed-Based National Pollutant Discharge Elimination System (NPDES)
Permitting Implementation Guidance. EPA 833-B-03-004.

https://www.epa.gov/sites/defauit/fiies/2015-09/documents/watershedpermitting finaiguidance.pdf.

EPA. August 2007. Watershed-Based National Poiiutant Discharge Elimination System (NPDES)
Permitting Technical Guidance. EPA 833-B-07-004. https://www.epa.gov/sites/default/files/2015-
09/documents/watershed techguidance entire.pdf.

Wisconsin DNR August 2010. Menomonee River Watershed: 2010 Water Quality Management Plan
Update. DNR Publication WT-950.

http://dnr.wi.gov/water/wsSWIMSDocument.ashx?documentSeqNo= 107575784.

Wisconsin DNR. September 2, 2014. Watershed Permitting Guidance. Guidance Number 3400-2014-
01. https://dnr.wi.gov/water/wsSWIMSDocument.ashx?documentSeqNo=102211149.

Wisconsin DNR and MMSD. March 19, 2018. Total Maximum Daily Loads for Total Phosphorus, Total
Suspended Solids, and Fecal Coliform: Milwaukee River Basin, Wisconsin. Final Report. CDM Smith.
https://dnr.wi.gov/water/wsSWI MSDocument.ashx?documentSeqNo= 158809714.

Wisconsin DNR. General Permit to Discharge Under the Wisconsin Pollutant Discharge Elimination
System. WPDES Permit Number WI-S065404-2. Issued March 31, 2020.


Wisconsin DNR. April 2020. Wisconsin Pollutant Discharge Elimination System Permit for Municipal
Separate Storm Sewer System, Permit No. WI-S065404-2: Fact Sheet - April 2020.
585859116953/Menomonee+Permit+Fact+Sheet+Final+4- 1-2020.pdf.

Watershed-Based Permitting Case Study — Menomonee River Watershed, Wisconsin

Wisconsin DNR. Wisconsin's Water Quality Report to Congress.

Wisconsin DNR. Water Condition Viewer.
https://dnrmaps.wi.gov/H5/?viewer=Water Condition Viewer.

Wisconsin DNR. Watershed - Menomonee River (Ml 03).


Permitting Authority Contact:

Samantha Katt

Wisconsin Department of Natural Resources (DNR), Permit Writer

Permit Type:

Multisource watershed-based permit

Permit Information:


e8649d0b1 b8041a19220d00/1585859028897/Menomonee+Permit+Fin
al+Sianed +4-1 -2020.pdf
Fact Sheet:

+ Sheet + Final+4-1 -2020.pdf

Pollutants of Concern In Watershed:

Total phosphorus, total suspended solids,
fecal coliform, and chloride

Pollutants Addressed In Permit:

Total phosphorus, total suspended solids,
fecal coliform, and salt/deicers

Permit Issued:

March 31, 2020

Watershed-Based Permitting Case Study

— Menomonee River Watershed, Wisconsin

March 2023