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Clean Water Act Water Quality Plans and Reports

Targeted Assessments of Wisconsin Water Resources

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Wisconsin's Clean Water Act water quality plans are published on an ongoing basis. Year 2020 plans listed below are final and approved. A list of reports scheduled for 2021 publication will be available shortly.

To learn more about a specific project or to get involved in your watershed, contact your local water quality program office.


2020 WQM plans

TWA WQ Plans and Monitoring Monitoring Project Overview
and Supplemental Documents
Watershed Information
(by Watershed Code)
Bear and Bluff Creek, Douglas County
Evaluation, 2018 St. Louis and Lower Nemadji River (LS01)
Bear Lake, Waupaca County
Effectiveness, 2017-2018 Lower Little Wolf River (WR06)
Beaver Creek, Dodge County
Evaluation, 2017-2018 Beaver Dam River (UR03)
Black and Little Black River, Douglas County
Evaluation, 2016-2017 Black and Upper Nemadji River (LS02)
East Twin River, Manitowoc and Kewaunee Counties
Evaluation, 2017 East Twin River Watershed (TK02)
Garners Creek, Outagamie County
Effectiveness, 2016 Plum and Kankapot Creeks (LF03)
Koshkonong Creek Jefferson, Rock & Walworth
Evaluation, 2016-2018 Upper Koshkonong Creek (LR12)
Lake Weyauwega, Waupaca County
Effectiveness, 2017 Waupaca River (WR05)
Legler School and Pioneer Valley, Green County
Effectiveness, 2017-2018 Little Sugar River (SP14)
Lower Little Wolf River Priority Watershed Water Quality Evaluation, Waupaca County

(See also: Lower Little Wolf 2017 TWA WQM Plan)
Effectiveness, 2015 Waupaca River (WR05)
Pecatonica River, Lafayette and Green Counties
Evaluation, 2015 Middle Pecatonica River (SP08)
Pigeon River, Waupaca County
Evaluation, 2015 Pigeon River (WR10)
Pine River, Waushara County
Evaluation, 2018 Pine and Willow Rivers (WR02)
Pipe Creek, Fond du Lac County
Effectiveness, 2018 Lake Winnebago - East (UF02)
Plum-Kankapot Creek, Brown County
Effectiveness, 2015 Fox River - Appleton (LF04)
Pokegama River, Douglas County
Evaluation, 2017-2018 St. Louis and Lower Nemadji River (LS01)
Sinsinawa River, Grant County
Evaluation, 2016 Galena River (GP01)
Soft Maple Hay Creek, Rusk County
Effectiveness, 2015-2016 Soft Maple and Hay Creeks (UC17)
South Fish Creek, Bayfield County
Evaluation, 2015 Fish Creek (LS08)
Upper East River, Brown County
Effectiveness, 2017-2018 East River (LF01)
Upper Fox Pebble, Waukesha County
Effectiveness, 2015-2016 Lower Fox River - Illinois (FX02)
West Branch Sugar River, Dane County
Evaluation, 2013 Allen Creek and Middle Sugar River (SP13) Watershed Planning
Wood River, Barrett Creek, Crex Meadows, Burnett County
Evaluation, 2014 Wood River (SC11)
Waupaca Tomorrow River, Portage and Waupaca Counties
Protection (Crystal River and Waupaca Chain of Lakes TWA), 2016-2017 Waupaca River (WR05)
Yellowstone River, Lafayette County
Evaluation, 2016 Yellowstone River (SP04)

TWA plan locations

Wisconsin targeted assessment water quality plan locations

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View TWA projects in an interactive map

The first of three sets of plans for review are located in blue below. The numbers on these plans correspond to watersheds with public review drafts posted in the 2020 WQM Plans tab.

Learn more about the state’s ongoing TWA studies.


2020 TWA/WQ plans and reports

TWA approach

Targeted watershed approach - streams, lakes, wetlands and more

TWA monitoring provides a rotating watershed approach for baseline data collection that blends baseline work with targeted and effectiveness monitoring.

Monitoring Objectives

The goal of targeted watershed assessments across lakes, streams, and wetlands is to identify attainment status and changes in water quality in response to land management practices. Initially, the focus of monitoring will be on streams, but lakes and wetlands will also be monitored in some targeted watersheds. The Targeted watershed approach aligns resource monitoring by watershed at HUC 12 or HUC 10 scale. The design is a rotation approach and its value is enhanced through alignment with fisheries monitoring. An additional value of this type of monitoring is the prospect of aligning volunteer monitoring with staff work to fill in gaps (spatial, temporal), conduct follow-up monitoring (TP sampling, AIS monitoring), collect strategic data (such as near permit outfalls, etc.) and to gather data that results in prioritization of new sites based on results. This approach can involve alignment and sequencing of monitoring, assessment, planning, implementation (i.e. watershed planning framework).

Monitoring Design

The TWA design involves monitoring at the HUC 12 scale (~29-mi2). Approximately five to six sites may be sampled per watershed (HUC 12) (1 site/5-mi2), at which chemistry, macroinvertebrates, fish, habitat, and flows/water levels. These core indicators will be supplemented by intensification areas at pour point including six grabs samples, one per month from May through October. Lakes will also be monitored in the Targeted Watershed when nutrient loading is a concern and/or when land management practices are in play. Water quality issues in lakes will often drive the interest in monitoring the condition of streams in the watershed and TWAs will integrate these two waterbody types.

Site Selection and Design

Stream monitoring locations were selected from a dataset of previously monitored reference sites and by best professional judgment. Although sites are meant to represent least-disturbed conditions because of the non-uniform distribution of land uses within the State the amount of agriculture and urban land uses in a specific reference watershed may vary across the State.

Monitoring for the Wadeable Trend Reference Sites requires multiple site visits to sample during the appropriate index periods. Temperature loggers should be deployed in spring as soon as the water levels are safe to work and removed in fall. Fish, chemical, physical habitat and flow monitoring should take place during the fish sampling summer index period avoiding recent rainfalls. The macroinvertebrate monitoring should occur during the fall sampling index period.

Water Quality Indicators

Targeted watershed approach indicators:

Lake water quality indicators will depend in part on the management practices in the watershed. Typical sampling will include: temperature, dissolved oxygen, conductivity profiles, Secchi depth, total phosphorus, chlorophyll a during spring overturn and three times during a summer index period (July 15 - September 15). Other parameters are collected based on situational factors such as site-specific discharges. Additional parameters include conductivity, pH, alkalinity, color and the nitrogen series. In addition, plant point-intercept surveys and habitat surveys may be conducted. Given resources, lake sediment cores, in-stream permit compliance and intermittent/ephemeral stream will be sampled. As needed, a lake water budget will be developed to understand nutrient loading.
Parameter Analysis location Database Assessment indicator
Chemistry Data State Laboratory of Hygiene Horizon (SLOH) to LDES to SWIMS TP package, chlorides package, and other (WisCALM assessment)
Macroinvertebrate IBI substrate sample UW Stevens Point Entomology Laboratory UWSP to SWIMS Wadeable macroinvertebrate index (WisCALM assessment)
Physical parameters In-field Fish database or SWIMS Physical (flow) data
Fish electroshock - fish species present, count In-field and fish database Fisheries database Fish IBI (dependent on natural community). (WisCALM assessment)
Habitat (qualitative) metrics In-field and fish database Fisheries database Habitat suitability index
Quality Assurance
  • Field protocols
  • In field Quality Assurance during data collection
  • Sampling & transmittal procedures
  • UWSP QA Processes
  • SLOH QA Processes
  • SWIMS Data flow QA checks
  • SWIMS Data Management Checks
  • Fish DB Data Quality Checks
Data Management

Field data is directly entered into the SWIMS system. Each HUC will be developed as its own "project" in the SWIMS system (data management design) and under each project fieldwork events with laboratory and field data are collected. Project set up and station creation is conducted in SWIMS by Rivers and Streams Program Coordinator or the SWIMS file manager. Field data is entered subsequent to the field data collection. The data entry into SWIMS follows the generation of labslips and the establishment of fieldwork events. Most analytical work is conducted at the State Laboratory of Hygiene and transmitted through the LDES to the SWIMs system.

Fisheries and habitat data is entered directly into the USGS supported Fisheries Database. Macroinvertebrate data is collected in the field and transmitted to the UWSP Entomology Laboratory for analysis. This data is then entered into a local computer and send to a contractor for the SWIMS system where it is entered into the SWIMS system and metrics are created. Currently, SWIMS does not store aquatic plant, habitat, sediment core, and water budget data on lakes. Plans to store aquatic plant and lake habitat data in SWIMS are under development.


Collected data will be summarized on a biennial basis for the purpose of reporting on the status of the state's waters for the Integrated Water Quality Report to Congress (every two years). The data will also be used for key parameter package analyses and statewide condition summaries. Of critical importance, all data from the Targeted Watershed Assessments (TWA) work will be rolled into the watershed planning assessments, narrative descriptions and recommendations will be entered and archived in the WATERS data on an ongoing basis. Biologists are responsible for completing reports for each Targeted Watershed on a schedule created by regional and central office.

Programmatic Evaluation

Periodic reviews to this study design will be made at two- and five-year intervals to determine if additional sites or subsequent monitoring is needed.