Biological monitoring of water in Minnesota

monitoring the biological health of streams photo of water bug

By measuring and evaluating the health of fish, macroinvertebrates, and plants, MPCA staff can distinguish between naturally occurring variation and changes caused by human activities.

Why perform biological monitoring?

The MPCA's water monitoring goals are tied to the goals of the 1972 Clean Water Act for restoring and protecting the multiple beneficial uses and ecological integrity of America's waters.

Primary goals

  • determine if stream water quality supports wildlife living in the streams (aquatic life)
  • determine if stream water quality supports swimming, wading, and boating (aquatic recreation)
  • determine if water quality is sufficient to eat fish caught in streams and rivers (aquatic consumption)
  • measure and compare regional differences in water quality
  • identify long-term trends in water quality

In the past, chemical criteria and related monitoring have been the traditional mechanism employed by regulatory agencies responsible for protecting aquatic life and assessing the condition of surface waters. Significant improvements in water quality have been made in the last several decades utilizing this approach.

However, human actions impact a wider range of water resource attributes than water chemistry alone can measure. The degradation of Minnesota’s surface waters can be attributed to a multitude of sources including: chemical pollutants from municipal and industrial point source discharges; agricultural runoff of pesticides, nutrients, and sediment; hydrologic alteration from stream channelization, dams, and artificial drainage; and habitat alteration from agricultural, urban, and residential development.

Biological communities are subjected to the cumulative effects of all activities and are continually integrating environmental conditions over time. They represent the condition of their aquatic environment.

Biological monitoring is often able to detect water quality impairments that other methods may miss or underestimate. It provides an effective tool for assessing water resource quality regardless of whether the impact is chemical, physical, or biological in nature. To ensure the integrity of surface waters, we must understand the relationship between human induced disturbances and their effect on aquatic resources.

MPCA and biological monitoring

The MPCA’s biological monitoring program was established in 1996. In its infancy the program consisted of three biologists roughly 50-100 river and stream stations were sampled annually. From 1996 to 2006 the organizing framework for random surveys was by major river basins, In addition to the random monitoring sites, a set of sites was selected to represent the range of human disturbance within each basin. Data from these ‘targeted’ sites helped create an adequate dataset that could be used for developing indicators and indexes of biological integrity (IBI),

In 2006, the agency received an LCMMR grant to design a watershed based monitoring plan. This new watershed approach was piloted on the Snake River Watershed in the St. Croix River Basin during the summer of 2006 and was followed by subsequent watershed studies in the Pomme de Terre River and North Fork Crow River Watersheds in 2007. In 2008, with the passage of the Clean Water, Land and Legacy Amendment, the MPCA would receive sufficient funding to implement the watershed approach across the entire state, with a goal to sample all of states watersheds over 10 years. Today, the agency’s monitoring program consists of more than a dozen biologists divided between the Brainerd regional office and MPCA Headquarters in St. Paul. Biologists sample roughly 500 streams and rivers annually under the Watershed Approach. In 2017 the agency’s biological monitoring program will have intensively sampled all of the states 81 major watersheds and 5 large rivers providing more complete picture of the condition of the health of Minnesota’s water resources.

How does MPCA work differ from DNR?



  • Assesses water quality
  • Uses fish and invertebrates as indicators of water quality
  • Conducts whole community fish surveys
  • Identify biological stressors
  • Manages game fish populations
  • Stocks fish
  • Stream restoration
  • Locates species of concern
  • Manages invasive species

While biological monitoring work done by the MPCA may appear similar to work completed by the DNR, there are distinct differences in the directive the two agencies have been given under state law.

There are some DNR offices that collect fish community data; this information is shared with MPCA and utilized for the assessment of water quality. The DNR is currently in the process of developing biological indicators for lakes including fish and plants; the MPCA is providing professional guidance. The DNR will oversee collection, while MPCA will provide the assessment for water quality.

Monitoring projects

Watershed approach

By 2006, only a small percentage of Minnesota's streams and rivers had been monitored for basic water quality. The MPCA decided it needed to examine more waterbodies at a faster rate, and developed what it calls the watershed approach.

The MPCA uses a 10-year cycle of intensively monitoring an average of eight watersheds a year. This monitoring includes lake water chemistry, and stream water chemistry and biological communities, such as fish and aquatic macroinvertebrate communities. The resulting data help determine if water bodies meet the standards for public health, recreation and aquatic life. This watershed approach allows the agency to examine more water bodies at a faster rate, by sampling near the outlets of watersheds of varying size (HUC 14, 12, 8 ) within the major watershed instead of sampling the entire watershed from its headwaters to its outlet. The first 10-year watershed monitoring cycle began in 2008 and will end in 2017.

Learn more about the watershed approach. Learn more about sampling design.

Large river monitoring

Piloted in 2013, with the Upper Mississippi River (headwaters to the St. Anthony dam), the MPCA’s Large River monitoring strategy  includes those large rivers not included in the original watershed approach: Mississippi River, Minnesota River, Rainy River, St. Croix River and Red River. These systems are complex, encompassing multiple watersheds and potential pollution contributions. Out of state inputs from watersheds in North Dakota, South Dakota, Wisconsin and Ontario, Canada, increases the complexity of river management.

Monitoring stations were selected in an unbiased manner placed at the borders of watersheds at varying scales (HUC 8,10,12) to better understand pollution sources from contributing watersheds. Stations are also placed up and downstream of wastewater treatment plant sources to monitor their compliance with water quality standards.

Learn more about large river monitoring.

Long-term Biological Monitoring Reference Stream Network

Started in 2013, the Long term Biological Monitoring Reference Stream Network is comprised 60 reference stations, monitored biennially, established to provide a better understanding of how reference condition changes over time due to climate change, The stations are evenly  divided across all of Minnesota’s ecoregions and stream types and were chosen due to their minimal or lack of anthropogenic stress.

In the short term, the network will help quantify temporal variability of bioindicators. Over time, the network will help detect and account for climate change impacts in aquatic life use assessment and stressor ID processes, while also enabling the assessment of reference site drift and potential need to re-evaluate aquatic life criteria.

Probabilistic rivers and streams survey

The MPCA conducts a statewide probabilistic rivers and streams survey every 5 years, randomly sampling 150 stations divided equally across the state’s three major eco-regions. The MPCA has conducted similar surveys since 1996; however, in past years surveys were not conducted statewide but rotated annually between Minnesota’s five major basins.

The survey work is funded in conjunction with EPA’s National Aquatic Resource Surveys (the National Rivers and Stream Assessments, formerly (EMAP)). As part of this program, EPA provides states additional funding to conduct monitoring efforts, MPCA utilizes these funds to complete this statewide random survey to develop trend information regarding the overall condition of the state’s rivers and streams.

Fish sampling

The fish survey typically includes four elements: fish sampling, a water chemistry sample, the Minnesota Stream Habitat Assessment (MSHA), and a brief assessment of potential stream stressors. The survey may also include a quantitative habitat assessment at stations which require additional monitoring. Information regarding MPCA survey methods can be found within the standard operating procedures (SOP) documents at the bottom of the page.

Fish sampling

Fish community information is collected at stream monitoring sites for the purpose of assessing water quality and developing biological criteria. Biological stations are established after spring field reconnaissance where sampling reaches are measured and marked off for future sampling, reaches are 35 times the mean stream width, ranging 150 meters up to 500 meters. During the index period of June through September, an objective survey is completed using electrofishing methods. All fish are collected, regardless of size, identified and returned to the stream after appropriate measurements are collected.

Water chemistry sample

A single-grab sample of water chemistry is collected to provide an understanding of condition during the biological sampling event. Continuous stream temperature monitoring is also conducted at select stations.

In-field measurements

  • pH
  • water temperature
  • conductivity
  • dissolved oxygen
  • dissolved oxygen saturation percent
  • secchi transparency

Laboratory measurements

  • total suspended solids (TSS)
  • total suspended volatile solids (TSVS)
  • total phosphorus (TP)
  • nitrite-nitrate (NO2+NO3)
  • ammonia (NH4)

Minnesota Stream Habitat Assessment (MSHA)

The MSHA provides a qualitative physical habitat assessment at stream monitoring sites looking at features of the surrounding land use, riparian zone, in-stream zone and channel morphology to better understand habitat conditions that may be impacting biological communities. Assessment information is utilized for the purpose of assessing water quality and developing biological criteria.

Stream Condition and Stressor Identification (SCSI)

SCSI is utilized in conjunction with the MSHA to provide a means to document general stream and riparian condition. SCSI assists in providing evidence of potential stressors and causal mechanisms that may be visible at time of sampling to better inform the Stressor Identification process.

Quantitative Stream Habitat Survey

MPCA’s quantitative habitat survey provides a more in-depth look at both in-stream and riparian habitat than the objective MSHA survey completed during all fish visits. Quantitative habitat surveys are conducted at stations requiring more intense monitoring efforts including stressor identification sites and problem investigations.

Habitat features are observed and quantified both longitudinally, measuring changes of in-stream features (riffle, run, pool, log jams, etc.) along the stream reach, and with a transect-based method where at thirteen evenly divided transects across the stream reach additional quantifiable measurements are collected. Collected measurements include: surrounding land use, water and sediment depth, canopy cover, erosion, habitat cover and riparian condition. This information is utilized for the purpose of assessing water quality, informing stressor identification and developing biological criteria.

Invertebrate sampling

The macroinvertebrate survey is comprised of three elements, a macroinvertebrate sample, a water chemistry grab sample and a Channel Condition and Stability Index (CCSI) Assessment. Information regarding MPCA survey methods can be found at the bottom of the page within the standard operating procedures (SOP) documents.

Macroinvertebrate sample

Macroinvertebrate community information is collected at stream monitoring sites for the purpose of assessing water quality and developing biological criteria. Sampling methodology involves a multi-habitat approach and entails collecting a composite sample from up to five different habitat types: hard bottom, aquatic macrophytes, undercut banks, snags or leaf packs. The goal of this method is to get a sample representative of the invertebrate community. Sampling consists of dividing 20 sampling efforts equally among the dominant, productive habitats present in the reach. The entire sample is preserved in ethyl alcohol and brought to a lab for identification.

Water chemistry sample

A single-grab sample of water chemistry is collected to provide an understanding of condition during the biological sampling event. Continuous stream temperature monitoring is also conducted at select stations.

In-field measurements:

  • pH
  • water temperature
  • conductivity
  • dissolved oxygen
  • dissolved oxygen saturation percent
  • Secchi transparency

Channel Condition and Stability Index (CCSI) assessment

The CCSI is used to assess physical indicators of channel condition and stability during biological sampling for stream assessments. This protocol was developed through consulting other existing channel stability assessments (Pfankuch 1975, Simon and Downes 1995, VANR 2007, Rosgen 2006, Ohio EPA 2007, Magner et al. 2010) and includes modifications that attempt to better characterize physical indicators of channel condition and stability observed in low- to mid-gradient streams in Minnesota.


The MPCA gathers water quality data from its staff, citizen volunteers, and partners, and then uses the data to assess the condition of Minnesota water bodies. This assessment is completed with cooperation from data collectors and focuses on whether or not waterbodies are meeting standards to protect for aquatic life, recreation and consumption to ultimately determine which streams are healthy and in need of protection and which are polluted and require restoration.

Starting in 2008, the MPCA began a 10-year cycle for intensively examining major watersheds or drainage areas. The MPCA is meeting its goals to study all 80 major watersheds within 10 years. Each intensive watershed study requires two years of data collection, assessments begin after data collection is complete and lag behind the 10-year monitoring cycle. Four to seven watersheds are assessed annually. Twenty-four watershed assessments have been completed as of 2013. An additional seven watersheds will be assessed in 2014, with the remaining watersheds scheduled through 2019.

Once assessments of basic water quality have been made, the monitoring data gathered during intensive monitoring serves as a starting point in determining the sources and magnitude of pollution for polluted waters, or as a baseline to set protection measures for waters meeting standards. State agency and local colleagues are partnering to conduct additional follow-up monitoring, including stressor identification, to develop Watershed Restoration and Protection Plans (WRAPPS). Learn more about Stressor Identification and WRAPPS. Through the Watershed Approach, intensive sampling and assessment of lakes and streams in all 81 major watersheds allows for better protection of Minnesota’s waters.

Use the interactive map below to visit watershed pages and view completed watershed assessment reports. Visit the MPCA's Environmental Data Access webpage for water quality data and assessments for individual rivers, streams and lakes.

Percent of assessed streams supporting aquatic recreation


Percent of assessed streams supporting aquatic life

  Map: Percent of assessed streams supporting aquatic life

Data and reporting

After assessing water quality data and determining if waters support aquatic life, recreation and consumption uses, the MPCA publishes its findings in detailed watershed reports and submits a draft list of impaired water bodies to the EPA.

Below are links to the MPCA's recent reports including  watershed monitoring and assessment reports. More detailed assessment information for individual streams can be found on the MPCA’s Environmental Data Access webpage.

Report title


The first ten-year cycle of sampling lakes and streams by watershed (the Watershed Approach) began in 2008, after two years of piloting the approach. To date, monitoring plans are fully on track. In 2017, all of the state’s watersheds will have been intensively monitored. In 2018, a second round of monitoring will begin to assess the progress of clean up and implementation effort.

  • 74 major watersheds have been intensively monitored.
  • An additional seven to eight watersheds will be monitored annually in subsequent years.

Intensive watershed monitoring

Goals to assess the stream water quality data from intensive watershed monitoring are also on track.

  • To date, water quality data from 54 out of 80 major watersheds have been assessed.
  • An additional 11 watersheds will be assessed starting in February 2017, with the remaining watersheds scheduled for assessment through 2019.
  • The most recent stream water quality assessments are shown below. More detailed assessment information for individual lakes can be found on the MPCA’s Environmental Data Access webpage.

In 2017, a new watershed monitoring cycle begins, which means returning to the watersheds that were monitored 10 years earlier. Re-monitoring reveals if water quality has improved, declined, or remained the same.

More about Minnesota's watersheds

Find out more about Minnesota's watersheds and the work that is being done.

Biological monitoring staff directory

Southern region




Kimberly Laing

Unit supervisor


Erin Andrews

Streams — Fish


Mike Bourdaghs

Wetlands — Plants


Joel Chirhart

Streams and wetlands —


Mike Feist

Streams — Fish


Dan Fettig

Streams — Fish


John Genet

Streams and wetlands —


Mark Gernes

Wetlands — Plants


April Lueck

Streams — Fish


Mel Markert

Streams — Fish


Brett Nagle

Streams — Fish


Aaron Onsrud

Streams — Fish


Northern region




Scott Niemela

Unit supervisor


Chad Anderson

Streams — Fish


Tony Dingmann

Streams — Fish


Dave Dollinger

Streams — Fish


Andrew Frank

Streams — Fish


Karsten Klimek

Streams — Fish


Ben Lundeen

Streams — Macroinvertebrates


Nathan Mielke

Streams — Fish


Jonathon Newkirk

Streams — Fish


John Sandberg

Streams — Fish


Nathan Sather

Streams — Macroinvertebrates