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Water quality monitoring



Wisconsin has 15,081 lakes, covering nearly 1 million acres. About 13,000 lakes are less than 50 acres, while only about 2,000 are greater than 50 acres. The Lakes Monitoring Program focuses primarily on assessing the status of larger lakes (>100 acres) with public boat access (including large river impoundments). Sampling of smaller lakes without public access is included on a reduced scale, due to staff and funding limitations.

  • Volunteer monitoring is the primary vehicle for data collection in Wisconsin. Citizen Lake Monitoring Network (CLMN) volunteers collect Secchi depth data on 670 lakes; chlorophyll-a and phosphorus data on 403 lakes, and dissolved oxygen on 244 lakes and temperature data on 377 lakes each year. Samples are collected once during spring overturn, and three times during the summer (June to Sept).
  • Lake planning and protection grants also design and collect water quality data. Trophic status is determined from summer average field collected Secchi depth or chlorophyll-a, and is used for primary lake assessment.
  • Satellite images are used to retrieve water clarity data for thousands of lakes in Wisconsin. The satellite retrieval of water clarity is limited to lakes at least five acres in size (51 % of Wisconsin's lakes). Lakes in which the Secchi depth is more than half of the maximum depth of the lake are excluded from the analysis to remove possible interference from the lake bottom. Satellite retrieved water clarity data are converted to Carlson's Trophic State Index (TSI) to determine a lake's trophic status.
  • Point-intercept (P-I) aquatic plant surveys are conducted annually on 40-50 lakes statewide on a stratified random basis. These surveys collect the data necessary to compute an Aquatic Macrophyte Community Index (AMCI).
  • Separate from the Baseline Lakes Monitoring Program, DNR staff conduct P-I surveys on numerous lakes as part of ongoing aquatic plant management activities. During 2005 and 2006, 163 lakes between 10-1500 acres (mean area = 230 acres) were surveyed. From these data, reference conditions for AMCI values have been developed for different lake classifications. In the future, targeted lakes grouped by natural community will be selected each summer to further refine the reference AMCI metric values and add to the aquatic plant database.
  • Water quality monitoring (TSI indicators, plus other parameters (Nseries, pH, alkalinity, color, conductivity ) is conducted on 65 Long-Term Trend (LTT) lakes statewide to monitor long-term trends and provide regional reference conditions for each defined lake class. These lakes help to characterize within-lake and among-year variability in baseline water quality monitoring (see the Surface Water Quality section of the Strategy for details). A program is also proposed for monitoring pathogens (E. coli) at high-use inland beaches (see the Pathogen Monitoring on Inland Beaches section).

Core and Supplemental Water Quality Indicators

  • Trophic Status Index (TSI): Satellite images are used to retrieve water clarity for the vast majority of lakes in Wisconsin simultaneously on a regular basis. Citizen Lake Monitoring Network volunteers collect Secchi depth data to calibrate a model for the retrieval of water clarity from satellite images for a sub-sample of the lakes in an image. This model is used for the retrieval of water clarity from thousands of lakes in the same image. Satellite retrieved water clarity data are used to compute the TSI and average summer TSI scores for a three year period are used to determine a lake's trophic status.
  • Reference values for TSI scores are estimated from sediment cores. Sediment cores allow a comparison of historical (pre-settlement) and recent water quality data in order to place modern day water clarity measurements in context and indicate changes in algal concentrations over time. Diatoms are a type of algae containing siliceous cell walls that fossilize in lake sediments. Diatom taxa are known to prefer narrow ranges of water quality and therefore the fossilized diatom community from the bottom of the core can be used to infer historical phosphorus concentrations or Secchi depth values. These inferred concentrations can then be converted to TSI values using the Carlson equations and used as reference values. This approach will not work for impoundments or raised wetland lakes. Since these lakes are artificial, pre-settlement conditions do not exist. Individual lakes are compared to expectations derived for each lake class based on the sediment core data set to determine lake health. Volunteers also assess pH and dissolved oxygen and temperature profiles during the period of peak summer stratification on a sub-sample of lakes. Trends in Secchi depth, phosphorus, and chlorophyll a are determined on a fixed set of approximately 150 lakes monitored by volunteers.

Aquatic Macrophyte Community Index (AMCI)

  • Native aquatic plant communities are recognized as a vital and necessary component of healthy aquatic ecosystems. Diverse and stable plant communities offer habitat for aquatic invertebrate and fish species and attenuate wave action, which minimizes shoreline erosion. Aquatic plants inhabit the littoral zone, the lake area most closely connected with direct anthropogenic habitat modification, and therefore are a good indicator of disturbance. Many recent studies in Wisconsin and Minnesota have shown that aquatic plant communities have been reduced in areas of shoreland development and have been altered by eutrophication.
  • The aquatic plant community are excellent indicators of in-lake, riparian, and watershed health for lakes. This metric is used primarily on small lakes, and is assessed once during the summer. Aquatic plants are also a lake biotic community that can be measured using standard, repeatable methods to estimate change over time and/or space. An aquatic macrophyte community index (AMCI) for Wisconsin has been developed by Nichols et. al. (2000) and has been shown to illustrate disturbance.


Wadeable Rivers

Natural Community Stratified-Random Monitoring

  • Tier I wadeable stream monitoring framework includes 200 sites randomly selected, stratified by the number of stream miles within each Natural Community Classification within each 8-digit Hydrologic Unit Code (comparable to DNRเน€เธ™€เน€เธ˜ย˜เน€เธ˜ย‚เน€เธ˜เธ‚เธขย™s Water Management Unit). Assessment information monitored at each site includes fish IBI, macroinvertebrate IBI, qualitative habitat, instantaneous temperature, pH, dissolved oxygen and conductivity. The collection of continuous temperature data is recommended if equipment is available. Data will be used to identify streams with poor biological condition ratings for additional sampling to evaluate potential for 303d listing. Condition assessments from individual stream sites may also be combined spatially and within stream natural community types to estimate the overall condition. For example, sufficient sites (~35 to 50) will have been sampled within a 5 year period, for each 8-digit HUC to draw conclusions about the condition of each of the natural community types within the basin. Site condition assessments can also be evaluated based upon different geomorphologic or land-use characteristics.

Natural Community Comprehensive Sites

  • Natural Community comprehensive monitoring including fish IBI, macroinvertebrate IBI, quantitative habitat, and base flow water chemistry (total phosphorus, ammonia nitrogen, nitrate-nitrite, total kjeldahl nitrogen) will occur at a subset of 50 sites. These 50 sites will be selected from the 200 randomly chosen NC Stratified Random sites for statewide condition assessment. This data will be used to report the condition of streams across the state and draw generalized inferences about pollutants affecting the quality of Wisconsins streams.

Wadeable Stream Long-term Trend Sites

  • Forty two wadeable stream sites will be monitored on annual basis to establish biological, physical and chemical trends over time. These sites will be selected from a suite of sites monitored in either 2008 or 2009 and include two sites in each of the following stream classes from each of the five WDNR regions:
  • Monitoring parameters at the long-term trend stream sites include fish IBI, macroinvertebrate IBI, quantitative habitat, and base flow water chemistry (total phosphorus, ammonia nitrogen, nitrate-nitrite, total Kjeldahl nitrogen). Data for these 42 sites will require 5 to 10 years of collection before a sufficient number of samples have been collected to evaluate trends. However, within a couple of years, the data may be used qualitatively to identify climatic years when trend reference data may vary dramatically from other years.

Watershed Rotation Water Quality Sites (Wadeable non-LTT)

  • These sites were selected and scheduled following a 6-year watershed (10-digit HUC) rotation framework where water samples were collected from multiple stations within a watershed from the largest เน€เธ™€เน€เธ˜ย˜เน€เธ˜ย‚เน€เธ˜เธ‚เธขยœpour point stream within that watershed. The intent of this monitoring effort was to capture water quality data from the largest drainage area from each watershed (ideally, at or near the mouth of each watershed). Monitoring sites were generally located in the furthest downstream reach of the largest wadeable stream in the watershed.
  • Water chemistry sampling was conducted at a 30-day interval (for example, every second Wednesday of the month) to avoid weather related bias. Field parameters included temperature, dissolved oxygen, pH and turbidity (using a turbidity tube). Lab parameters will include total phosphorus, ammonia-N, total Kjeldahl-N, nitrite-nitrate-N and suspended solids. During fiscal year 2012, sites will be monitored until the end of the water year (September 2011).

Non-Wadeable Rivers

Long-Term Trend River Sites (Nonwadeable LTT)

  • The current Long-term Trend (LTT) water quality-monitoring network, rejuvenated in 2001, consists of 42 sites, with a minimum of one site per major river basin, generally located near the mouth of each river. Most of these sites were part of an earlier trend monitoring program with data available from as far back as the 1970s. Selection of the 42 trend monitoring sites considered different land coverage in the state varying from urban areas in the southeast, heavy agricultural use in central and southwest and forest cover dominating in the north. Just over half the sites (24) are sampled monthly and the other sites are sampled quarterly.
  • Monthly sites are generally located near the mouth of major rivers, whereas, quarterly sites are often located at additional sites on major rivers some distance above the mouth. The number of water quality measurements for some sites on the Mississippi River (Lock and Dams (LD) 3 and 4) were reduced due to the availability of monitoring data from other agencies. Water quality samples are analyzed for nutrients, solids, specific conductance, pH, hardness, alkalinity, bacteria, chlorophyll, and biannually for triazine herbicides following approved U.S. EPA methods. Low level metal sampling using clean hand techniques is conducted quarterly at a subset of the monthly monitoring sites and biannual sampling of triazine is done during winter and summer periods.

Large River Macroinvertebrate Sites (Biotic Integrity River Sites)

  • From 2002 to 2006, between 86 and 111 river stations were sampled for fish IBI plus an additional 44 to 62 river stations were sampled for gamefish-endangered-threatened (GET) species. This sampling was conducted primarily by Bureau of Fisheries Management staff and supplemented by ISS staff, and in SCR region by Watershed Bureau staff. During this same time, macroinvertebrate samples were collected from 125 sites and used to develop a nonwadeable rivers macroinvertebrate IBI (Weigel and Dimick, In press).
  • In 2011, the Watershed Bureau started an 8 year program to revisit 125 river sites including five sites that are sampled each year (long-term trend sites) and 15 rotational sites. The five long-term trend sites represents least-impacted conditions based upon previous sampling results and watershed condition knowledge of biologists. Three rotational sites per region will be selected for sampling each year. Hester Dendy artificial substrates (3 per site) were be placed at the sites for six weeks and the samples of colonizing macroinvertebrates processed at the UW-Stevens Point Entomology Laboratory using a 500-target sub-sorting procedure plus a large-rare taxa search.
  • The Bureau of Fisheries Management will the use of fish-IBI data for large river condition assessment will be on a case by case basis. The data will be compared to historical data collected prior to 2006 to determine if large river conditions have changed. Sites with poor macroinvertebrate IBIs will be flagged for comprehensive sampling in order to evaluate their potential as 303d impaired waters. In addition, within three to five years of collection, a sufficient number of samples (~50 to 75) will be collected to make inferences about the condition of Wisconsin rivers.

River Annual Sites (Non-wadeable, Non-LTT)

  • Of a total of 125 sites originally monitored for fish and macroinvertebrate IBIs from 2003 and 2006, 89 sites were selected for water chemistry monitoring from large river (non-wadeable) sites that were not in close proximity to Long-Term Trends monitoring sites. The River Rotation sites are monitored monthly for one water year (12 months). Sampling dates are selected approximately 30 days apart and samples are collected regardless of flow conditions. Sample parameters include field temperature, dissolved oxygen, pH and turbidity (using a turbidity tube) and laboratory analysis including total phosphorus, ammonia-N, total Kjeldahl-N, nitrite-nitrate-N and suspended solids.

Continuous Flow Gauging Stations

  • WDNR has funded selected USGS flow gauging sites since the 1970s. Some of these sites have data records for over 100 years. WDNR directly funds 14 of 120 USGS long-term gages statewide as well as short-term gauging stations to support development of Total Maximum Daily Loads (TMDLs). USGS supplies all staff time for this monitoring program.
  • WDNR assists in the operation of a statewide network of 126 permanent USGS continuous-stream flow gaging sites, some of which have data records for over 100 years (Figure 3). Many of these sites are also the locations of WDNRs Long Term Trends monitoring stations shown in Figure 2. Though WDNR funds only a portion of these sites, data are available from the entire network of long-term sites. Water-Stage Recorders and Acoustic Velocity Meter (AVM) Systems are used depending on site conditions. All sampling is automated, with water level recorded every 15 minutes. Approximately eight times each year, USGS staff also conduct in-field flow measurements to check the accuracy of the rating curve. Data are downloaded every day. Regressions based on data collected at fixed sites are used to develop estimates of critical flows at needed ungaged locations statewide.
  • WDNR cooperates with USGS and their other cooperators to select the long-term gaging sites. A major review and planning effort was undertaken by the USGS and their cooperators with support from University of Wisconsin professors in the mid-1990s when funding for the statewide network was being cut by the WNDR due to budget problems. A resulting 1998 UW Water Resources Institute report documented the need and uses for the statewide network and recommended specific sites and funding sources. WDNR funds sites of unique interest to us as well as other sites to provide adequate coverage for development of regressions at ungaged locations.

Baseline Wadeable Streams Monitoring

  • From 2000-2004, the Baseline Wadeable Streams Monitoring Program incorporated a targeted sampling design where Region biologists picked assessment sites to disperse the sampling effort among streams of differing size (stream order) and temperature regimes (cold water and warm water fish communities). Beginning in the 2005 field season, a probability-based sampling design was incorporated to randomly select stream assessment reaches from stream classes (groupings of streams with similar ecological potential). WDNRs stream resources. Given the large number of small streams in Wisconsin, it is necessary to sub-sample these populations of streams, where as it may be possible to census populations of higher order streams (Table 3). Data gathered from sub-sampled 1st and 2nd order streams will be used to make inferences for all small streams within their respective classes. If necessary, third order and larger stream populations will be sub-sampled and inferences made of physical, chemical, and biological integrity for all larger streams as well. Sub-sampling designs will be developed to meet specific data quality objectives for the Departments multiple resource assessment and management objectives. Intermittent streams are not sampled at this time due to limited resources (see Program Gaps). Geographic Information System (GIS) technology will be used to characterize land use, and other measures of factors impacting stream integrity, to proportionally direct greater sampling effort to stream classes where environmental health is at greatest risk.
  • The basic sampling unit will be assessment reaches within stream classes. These reaches are best described as: 1) small (1st order) coldwater; 2) small (1st and 2nd order) warmwater; 3) large (2nd order and larger) coldwater; and 4) large (3rd order and larger) warmwater.



The wetlands monitoring design will incorporate theเน€เธ™€เน€เธ˜ย˜เน€เธ˜ย‚เน€เธ˜เธ‚เธขยœthree tier framework endorsed by the USEPA National Wetland Monitoring Workgroup to efficiently gather scientifically valid information that meets the needs of managers. Level 1, landscape assessment, relies on coarse, landscape scale inventory data typically gathered by remote sensing and available in a GIS format, such as the Digital Wisconsin Wetland Inventory, Reed Canary Grass Infestation Map, Potentially Restorable Wetlands Maps and Potential Ephemeral Ponds Maps. Level 2, rapid assessment, consists of relatively simple rapid protocols to be conducted at specific sites. The Department will be revising and supplementing the Wisconsin Rapid Assessment Method as a level 2 assessment tool. Level 3, intensive site assessment, uses intensive ecological measures to score the relative condition of a site, based on research-derived indices of biological integrity. Due to likely funding limitations and the need to tie wetlands assessment to watershed planning, Department management structure, and restoration opportunities, it is recommended that implementation of a formal wetland monitoring program be conducted on a rotating basin or rotating watershed basis; with assessment at the basin or watershed scale. The number of sites needed for representative coverage and sampling frequency for future level 2 and 3 assessments is still to be decided.

Extensive landscape level assessment using available GIS wetland inventory, hydrography soils and landuse/ land cover data for coarse assessment, supplemented by follow-up rapid and intensive site assessments, is contemplated at the Basin (equivalent to 8 digit hydrologic units (HU)) scale. The initial focus will be to identify wetland restoration opportunities and characterize wetland condition at the watershed (10 digit HU) and subwatershed (12 digit HU) level. Monitoring design will be guided by the lessons learned in current pilot projects in the Milwaukee River Basin and in the Mead Lake watershed. Implementation will depend upon continued federal and state funding.

Core Indicators
  • Occurrence and abundance of reed canary grass (Phalaris arundinacea) monotypic areas 30m resolution acre minimum mapping unit; occurrence of other wetland invasives such as purple loosestrife (Lythrum salicaria) and giant reed grass (Phragmites australis) to characterize condition of the plant community.
  • Watershed Functional Assessment methodologies adapted from the Milwaukee River Basin Wetland Assessment Project will provide key wetland information for watershed planning. This would include identification of potentially restorable wetlands, estimates of wetland loss, estimates of wetland percent of original watershed and sub-watersheds, need for restoration, relative estimates of some specific ecosystem services (functions) remaining, targeting of restoration opportunities to maximize specific ecosystem services, and analysis of some functional consequences of alternative development scenarios.
  • Floristic Quality Assessment (FQA) scores: Floristic Quality Index (FQI) and Mean Site Conservatism (mean C) for intensive (Level 3) site surveys to characterize condition of the plant community of any wetland type.
  • Indices of Biological Integrity (IBIs) for isolated depressional wetlands, based on plants, macroinvertebrates, zooplankton, diatoms, and amphibians have been developed for intensive (Level 3) site surveys to characterize biological condition. Level 3 methods for other wetland types are not yet available.

Fish Tissue

Fish Tissue

Each year the WDNR collects and analyzes samples of fish tissue from Wisconsins inland waters and the Great Lakes, including their tributary streams. The objectives of the fish contaminant program include protection of fish consumers by determining the levels of bioaccumulatory contaminants in the edible portions of fi sh and comparing these levels to health guidelines, as determined by the Wisconsin Division of Health. Samples are collected and/or analyzed by WDNR as a part of normal fish contaminant monitoring by cooperators like the Great Lakes Indian Fish and Wildlife Commission (GLIFWC), the USEPA, or as a part of special projects and research. For more information see the fish advice website.

Samples from the Great Lakes are analyzed for polychlorinated biphenyls (PCBs), pesticides, and mercury, while samples from river systems are primarily analyzed for PCBs and mercury. Fish samples from inland lakes are analyzed almost exclusively for mercury. Fish consumption advisories are issued for certain species and sizes of fish from given areas where the concentrations of chemicals in the fish flesh exceed the health advisory levels. Fish contaminant data are also used to make natural resource and environmental management decisions.

Statewide General Fish Consumption Advisories

Wisconsin issues general advice that applies to most inland waters where mercury concentrations or other pollutants do not require more stringent advice. Th e general advisory issued in 2002 is based on US EPAเน€เธ™€เน€เธ˜ย˜เน€เธ˜ย‚เน€เธ˜เธ‚เธขย™s reference doses for mercury and typical levels of mercury found in Wisconsin fi sh, based on the mercury concentration data that Wisconsin amassed over the last 30 years. Fish Consumption Advice.

Specific Fish Consumption Advisories

In addition to the general advisory that applies to most inland waters, more stringent consumption advice applies to specific waters in which fish have been found containing higher concentrations of mercury, or PCBs and other pollutants. These are waters for which testing indicated the presence of PCBs, dioxin/furans, and perflourochemicals. Additionally, more stringent advice applies to some species in specific surface waters due to higher concentrations of mercury. The number of sites with fish consumption advice has changed over the years, in part due to monitoring, banning and limiting chemical usages, and modification of the protocols used to determine appropriate advice. More information on collecting fish tissue samples and analylsis can be found in Attachment C (WisCALM).



Great Lakes Beaches

The federal Beaches Environmental Assessment and Coastal Health (BEACH) Act, was passed in October 2000. The BEACH Act requires States that border the Great Lakes or other coastal areas to develop beach monitoring programs, and a process for notifying the public about beach conditions. Wisconsin receives an annual allotment from USEPA to continue developing and implementing Wisconsin's Beach Monitoring and Notification Program. Wisconsin has approximately 55 miles of public beach and a total of 192 coastal beaches along the shores of Lake Michigan and Superior. The definition of beach for the purpose of Wisconsin BEACH Act implementation is: A publicly owned shoreline or land area, not contained in a man-made structure, located on the shore of Lake Michigan or Lake Superior, that is used for swimming, recreational bathing or other water contact recreational activity.

Wisconsin Beach Monitoring and Notification Program was developed to reduce the risk of exposure of beach users to disease causing microorganisms in water. Wisconsin was one of the first states to develop their program in 2003 and has been a model program for other states. Selected beaches along the Great Lakes are monitored for E. coli bacteria in accordance with BEACH Act requirements. Since 2003, WDNR has worked closely with approximately 16 local health departments, university researchers, the State Lab of Hygiene, and the United States Geological Survey (USGS) to monitor approximately 123 sites along the shorelines of Lake Michigan and Lake Superior. Read more about pathogens and Beach Health.

Photos - Slideshows

Last revised: Tuesday May 30 2017