Yahara Lakes of Dane County

The Yahara Lakes are a chain of five lakes connected by the Yahara River, located in Dane County, Wisconsin. The lakes are some of the most visible symbols of Madison and the surrounding areas and are at the heart of the area’s recreation, tourism, ecosystems and natural beauty.
Unfortunately, the lakes have historically faced challenges from several pollutants as a result of intense land use in the surrounding area. One pollutant in particular, phosphorus, leads to the algae blooms that blanket the lakes each summer.[1] These algae blooms are ugly, foul-smelling, and can be toxic to humans and animals. They result in closed beaches, reduced opportunities for recreation like boating and fishing, and threaten the health of local ecosystems.
Today, Clean Wisconsin and other organizations are working hard to ensure that the Yahara Lakes are clean, safe, beautiful places for everyone to enjoy.

Key Points

  • The five main Yahara Lakes and the Yahara River that connects them provide recreational, aesthetic, and economic value to Dane County and the city of Madison.
  • Algae blooms caused by excessive amounts of phosphorus pollution running into the lakes resulted in over a hundred days of beach closure in 2011.
  • The Yahara Watershed contains some of the largest remaining wetlands in Dane County, and provides homes to many rare species of plants and animals
  • Clean Wisconsin is working with several partners in an effort to clean up the Yahara Lakes through the first adaptive management pilot project in the state.
Clean Wisconsin's Work

As the Yahara lakes have had noticeable water quality issues for decades, the lakes have also been the subject of considerable research and cleanup efforts to date. Lake Mendota is one of the most studied lakes in the world, providing scientists and decision-makers with significant background information on lake quality and how it got that way. Concerned citizens and stakeholders have also organized efforts around water quality improvement before the passage of the phosphorus rules. Some past and ongoing management initiatives for the lake include the Yahara Lakes Legacy Partnership (YLLP), a joint initiative between several municipalities, agencies and nonprofit organizations, and the Rock River Basin TMDL, an EPA-approved management tool that limits the amount of phosphorus that water bodies in the Rock River Basin (including the Yahara Lakes) may receive each day. Additionally, the Yahara CLEAN partnership released a report in 2010 that includes 70 possible actions for cleaning up the Yahara Lakes. It was later condensed into a strategic action plan, released in 2012 through the Clean Lakes Alliance, with 14 recommended actions for water quality improvements.

With the passage of the phosphorus rule in 2010, there was now an additional regulatory driver to reduce phosphorus pollution entering the Yahara Lakes. Madison Metropolitan Sewerage District (MMSD), as one of the only permitted point sources in the Yahara watershed, was now facing a much more stringent phosphorus limit for its wastewater discharge. MMSD weighed its compliance options for meeting this limit, which include facility upgrades, water quality trading, and the adaptive management option (AMO), based on the relative costs and benefits of each option. Based on this evaluation, the AMO has the potential to be the most cost-effective and beneficial compliance option for MMSD and the community. MMSD is now implementing a pilot project to evaluate the AMO’s feasibility as its official compliance strategy.

The Yahara AMO Pilot Project
MMSD, along with several partners in the area, is midway through a four-year pilot project to determine whether the AMO will be a feasible and cost-effective compliance option for MMSD. This effort, referred to as Yahara Watershed Improvement Network (Yahara WINs), is the first AMO pilot project in Wisconsin. The project will be the basis for MMSD deciding whether it will choose the AMO as its compliance option by the time the facility’s permit is renewed in 2015.

Who’s Involved?
Besides MMSD, there are 30 other signatories to the project Memorandum of Understanding (MOU), including Clean Wisconsin. Many of these signatories are other local municipalities that are customers of MMSD, so they’re interested in the AMO’s potential to save phosphorus reduction costs. Additional partners in the project include environmental groups (the Clean Lakes Alliance and Sand County Foundation) and the Dane County Land and Water Conservation Department. On the agricultural side, a farmers’ group called Yahara Pride came together to encourage and organize the adoption of best management practices in the pilot project area and beyond.

How much does it cost?
The project is estimated to cost $3 million,[5] with funding covered by signatories to the MOU in proportion to their respective phosphorus contribution to the watershed. However, a large portion of the funding is covered by a $1.3 million grant from the Mississippi River Basin Initiative (MRBI), a federal program that supports conservation efforts for the Mississippi River and its tributaries. This grant is an example of the several programs and grants available to support runoff reduction efforts, one of the benefits of the AMO.

How is the project being implemented?
The Yahara pilot project kicked off in 2012. The first few years of this project have focused on activities that lay the groundwork for the AMO, such as outreach to potential urban and rural partners. Through its initial outreach, MMSD contacted several area municipalities to show the potential benefits and cost savings of the AMO for the watershed. Meanwhile, the Dane County Land and Water Conservation Department started working with area farmers to take inventory of current agricultural management practices and find opportunities for phosphorus reductions through practices on the land.

Another important component of watershed planning – and a requirement of the AMO – is setting up a monitoring program to measure the phosphorus reductions accomplished through practices implemented on the ground. To establish baseline phosphorus levels for the Yahara project and measure reductions, the Yahara project is using a combination of high-tech water quality gauges provided by the U.S. Geological Service (USGS) and water sampling by volunteer stream monitors. This data will be a key factor in evaluating the effectiveness of the project in reducing phosphorus loadings to water bodies.

Along with outreach and monitoring, the project has also begun implementation of on-the-ground practices to reduce phosphorus loss. Yahara WINs provided funding to Yahara Pride to implement a cover crop program, in which agricultural fields are planted over the winter to prevent soil and nutrient loss with runoff. Over the next few years of the project, Yahara WINs will continue to support practices that manage manure and reduce surface runoff, called best management practices (BMPs). Meanwhile, ongoing and expanded water monitoring will demonstrate the real-world effects of these practices.

For additional information about the Yahara pilot project, visit the project page on MMSD’s website, http://www.madsewer.org/Programs-Initiatives/Yahara-WINs.

Clean Wisconsin’s handbook on the AMO also contains a description of the Yahara pilot project. Because the pilot project is in progress, the project is evolving and lessons from the project are still emerging. In this project, as in others, it will take time to see the real-world impacts of practices implemented today. As the project evolves, we’ll update this page and the handbook with lessons learned and successes from the Yahara project that can be applied to the AMO around the state.

Questions and Answers

What are the Yahara Lakes?

The Yahara lakes are a chain of lakes connected by the Yahara River located in and around Dane County.  These lakes include Lake Mendota, Lake Monona, Lake Wingra, Upper Mud Lake, Lake Waubesa, (Lower) Mud Lake, and Lake Kegonsa.[4]The last glacier to move through the area 10,000 years ago formed these lakes by depositing glacial till and damming up the pre-glacial Yahara River Valley.  Today, the watershed covers 359 square miles with the Yahara River beginning at the edge of Columbia County, traveling through Dane County to connect the lakes, and connecting up with the Rock River in Rock County.[2]

What makes Yahara Lakes watershed special?

The Yahara Lakes watershed has many unique characteristics that shape its ecology and water quality.  The Yahara Watershed has rich soils, which are especially valuable for farming, as a result of its glacial and geological history.  At the same time, the watershed contains some of the largest wetlands in Dane County, including Cherokee Marsh, which is located at the head of the chain of lakes.  These wetlands provide storm water storage, filter out harmful toxins, and act as nutrient reservoirs, supplying a unique habitat for many endangered plants and animals.[3]

How does land use in the Yahara Watershed impact the lakes?

Dane County is home to a mix of intensive agriculture and urban growth, both of which have contributed to phosphorus pollution in the Yahara lakes. The watershed is home to about 350,000 people and contains parts of five cities, seven villages, and 16 towns as well as most of the urbanized land of the Madison metropolitan area. On the urban side, phosphorus pollution comes from point sources like wastewater treatment facilities and industrial dischargers, as well as runoff of stormwater from surfaces like lawns, streets and parking lots. On the rural side, phosphorus runs off farm fields, barnyards and natural areas and enters streams that feed into the Yahara River and the lakes.

What is the Yahara WINs pilot project?

In response to newly established water quality criteria for the Rock River Basin, the Madison Metropolitan Sewerage District (MMSD) and Dane County have partnered with local farmers, communities, and other parties and to work toward reducing polluted runoff in the Yahara Watershed.  These partners recently announced a pilot project created to evaluate multiple different strategies for reducing phosphorus runoff and determine the most efficient and cost effective ways to reduce phosphorus pollution.  Strategies include phosphorus adaptive management and implementation of a mix of agricultural and urban best management practices.  The initial pilot project will be conducted in the Six Mile Creek Watershed, last for 4 years (2012-2015), and cost $3 million.[5] The project aims to reduce phosphorus runoff by 1lb/acre/year adding up to over 20,000 pounds by the end of 2015.[6]

What is a ‘cow power” facility and how does it work?

A “cow power” facility is a name for a type of manure digester that generates renewable energy. These facilities function by heating the manure in an airtight tank to encourage bacteria to break down the manure, which produces methane. In turn, the methane gas is used to produce energy. Certain types of digesters, including the digester northwest of Madison, also remove phosphorus from the manure. The Dane County digester separates the liquid and solid components of manure, removing about 60 percent of the phosphorus from the waste. The reduced-phosphorus liquid component is then returned to farm fields, while the separated solid waste provides a phosphorus-rich compost or fertilizer that can be used for landscaping or gardening.

How is Dane County using biodigesters to improve our community and protect our lakes?

In 2010, as part of an initiative to reduce phosphorus pollution in the Yahara Watershed, Dane County partnered with Clear Horizons, LLC (a biogas energy company) and three dairy farms just north of Waunakee to create the county’s first manure digester. Currently, Dane County is partnering with U.S. Biogas (as project developer) and three dairy farms (Ziegler Dairy Farm, Blue Star Dairy, and the Hensen Brothers dairy farm) to create a second digester just outside of Middleton. These projects help reduce phosphorus pollution from runoff in the lakes, contribute to clean energy initiatives by powering area homes, and create jobs in Dane County.

Where can I learn more about the characteristics and conditions of these lakes?

Scientific data on current conditions in lakes and rivers across the Yahara River watershed can be found at the INFOS system website, http://infosyahara.org.

The University of Wisconsin’s Center for Limnology has information on characteristics as well as typical conditions of Lake Mendota and other Yahara Lakes at their website for lake information.

Quick Facts
  • There are five main lakes (Mendota, Menona, Wingra, Waubesa, and Kegonsa) in the Dane County Yahara Chain of Lakes, connected by the Yahara River. Another two lakes (Upper Mud Lake and Lower Mud Lake, both bordering Lake Waubesa) are also sometimes considered part of the chain.
  • The Yahara watershed, created over 10,000 years ago by the last glacier, covers 359 square miles.[2]
  • The Yahara Watershed contains some of the largest remaining wetlands in Dane County, and provides homes to many rare species of plants and animals.[3]
  • As early as 1882, the first noxious growth of algae was noted by local citizens.[1]
  • The 15 major beaches in the chain of lakes saw 107 days and 72 days of beach closure in 2010 and 2011 respectively as a result of E. coli and blue green algae.[1]
  • There has been a trend toward heavier rainfalls in recent years, resulting in increasing amounts of polluted runoff into the lakes.[1]
Wisconsin Data, Trends, and Legislation

Timeline of Yahara Lakes Protection and Management

Dane County has been working for decades to manage the Yahara lakes watershed, reduce nutrient and pollutant loadings, and provide institutional coordination and support for lake improvement. As part of the Priority Watershed Program, a statewide initiative to improving water quality in targeted watersheds, the county implemented Priority Watershed Projects in 1981, 1988, and 1993 that focused on on Lake Mendota and the Yahara River. Since then, several new initiatives have begun to protect and improve the Yahara Lakes.


The first noxious growth of algae was noted by local citizens.[1]


Lake Mendota Priority Watershed Project – promoted erosion control in agricultural areas and storm-water management in urban communities.[1]


Priority Watershed Project for the Yahara River and Lake Monona Watershed – reduced agricultural sources of sediment by 48%.[1]

1993 to 2008

Yahara Mendota Priority Watershed Project – promoted traditional conservation practices such as grass waterways, contour strip cropping, stream-bank protection, barnyard runoff systems, nutrient management, and wetland restoration in the watershed for Lake Mendota.[1]


Clean Wisconsin and the Gathering Waters Conservancy partner with the Yahara Lakes Legacy Partnership to create a report on the Yahara Lakes funded by the Madison Community Foundation.


Yahara CLEAN is established with the Memorandum of Understanding.


The first manure digester (“cow power” facility) is put into operation in Waunakee by Clear Horizons, LLC,

The Wisconsin phosphorus rules passed.


The Dane County Water Partnership is announced.  It establishes goals to create a second “Cow Power” facility, work with farmers to implement best management practices to reduce phosphorus runoff, and partner with municipalities to retrofit pipelines and storm drains to reduce polluted runoff.[1]


The Yahara Lakes Water Level Advisory Group published its Final Recommendations Report.


Projected timeline for the Madison Metropolitan Sewerage District’s Yahara WINs pilot project, which has a goal of demonstrating the feasibility of the AMO in the Yahara watershed.

 Current Law

There are several state and local laws and regulations that apply to the Yahara Lakes and practices that contribute to phosphorus pollution. Notably among these is the rule package referred to as the phosphorus rules, which set numeric criteria for phosphorus in water bodies and options that permitted facilities have to meet those criteria. These rules are outlines in Wisconsin Administrative Code chapters NR 102, 151 and 217.

In addition to statewide laws, Dane County has a number of local regulations dealing with nutrient control. For example, in 2004, then-County Executive Kathleen Falk signed a county ordinance restricting the sale and application of phosphorus-containing lawn fertilizers. More information about this ordinance is available at http://www.danewaters.com/management/phosphorus.aspx.

On the agricultural side, Dane County also has local ordinances related to manure management, including standards for manure storage and application. For example, following a runoff event in 2005 that led to a fish kill, Dane County passed an ordinance restricting the application of manure to frozen ground (a practice that increases the potential for surface runoff). More information about Dane County’s manure management ordinances is available at http://www.countyofdane.com/lwrd/landconservation/manure.aspx.

Cited Resources
  1. State of the Yahara Lakes 2011 Report (Clean Lakes Alliance)
  2. Yahara Lakes History and Setting (Dane County Office of Lakes and Watersheds)
  3. Yahara Waterways Water Trail Guide
  4. Lake Info (Yahara Lakes Association)
  5. Yahara WINs Pilot Project Handout (Madison Metropolitan Sewerage District)
  6. Yahara WINs Adaptive Management Pilot Project Work Plan Summary (Madison Metropolitan Sewerage District)


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Please cite this resource as: Clean Wisconsin, Inc. “Yahara Lakes of Dane County.” Clean Wisconsin Enviropedia. Retrieved from www.cleanwisconsin.org/enviropedia.