Watershed sampling design: Intensive watershed monitoring

In order to effectively sample streams throughout the state, the Intensive Watershed Monitoring Plan was designed to assess the aquatic health of the entire major watershed through intensive biological and water chemistry sampling.

Intensive Watershed Monitoring utilizes a ‘pour point’ method of sampling; this systematic sampling near the mouth of watersheds of different size scales is used to measure the condition of the upstream watershed in an unbiased way. The intensive approach allows assessment of the watershed for aquatic life, aquatic recreation, and aquatic consumption use support of the state’s streams in each of the state’s 80 major watersheds on a rotating 10 year cycle. These uses are assessed to make sure that the goals of the Clean Water Act are being met; having “fishable, swimmable” waters.

The main objectives of the Intensive Watershed Monitoring Strategy are to determine the condition of all watersheds throughout the state for a variety of indicators, to locate watersheds with impairments, to provide information for the stressor identification/TMDL process, and to monitor conditions over time.


The watershed design was introduced in 2006 with sampling of the Snake watershed, and sampling has been completed in the Pomme de Terre, North Fork Crow, Le Sueur, Root, Little Fork, Sauk, Mississippi River-Red Wing, Tamarac, and the Upper Red River watersheds. Sites are sampled in three categories; biological, water chemistry, and fish contaminants. Starting in 2009, lakes will be sampled along with streams in the watershed design. Watershed sampling takes place over a number of years, with the first year (Phase 1) focusing on identifying problems and the second year (Phase 2) focusing on investigating and identifying the sources of impairments.


When selecting sites, natural stream reaches are preferred over channelized stream reaches. Sites are placed near road crossings at least one mile from larger bodies of water such as lakes, wetlands, and rivers. These sites are chosen to avoid the collection of fish species that generally inhabit larger bodies of water, thus reducing the measurability of the upstream water condition. Sites are not selected in minor watersheds with drainage areas less than 5 sq. miles. The number of sites per watershed increases as the size of the watershed increases. Biological, Water Chemistry, and Fish Contaminant indicators are monitored to determine the condition for all watersheds.

Biological sampling

The majority of the sites in the watershed design are termed biological (signified by red dots). A single water chemistry sample will be taken at each of these sites during the summer, but the major emphasis of these sites is biological sampling of the fish and invertebrate communities for the determination of aquatic life use support. Fish are sampled through electro-shocking, and invertebrates are sampled with dip nets. Sites are placed at the nearest road crossing to the end of each minor watershed throughout the larger watershed to be able to assess the watershed for biology. Sampling does not take place in a minor watershed if a lake, wetland, or larger stream is within one mile of the planned site location.

Water chemistry sampling

At the end of each 11-digit hydrologic geographic unit (called a HUC), a water chemistry site is placed (signified by green dots). These sites are sampled for biology, along with an increased water chemistry component. Sites are sampled ten times throughout the summer, and depending on the watershed, may be sampled for nitrates-nitrites, ammonia, dissolved oxygen, pH, conductivity, temperature, total phosphorus, Kjeldahl nitrogen, chlorides, sulfates, calcium, magnesium, total suspended solids, total volatile solids, E. coli, chlorophyll-a, pheophytin, and transparency data. E. coli data makes it possible to assess the stream for aquatic recreation, and dissolved oxygen, transparency, and suspended solids data makes it possible to assess the stream for aquatic life.

Fish contaminants sampling

At the pour point of each of the major watersheds, fish are collected for the analysis of contaminants (mercury and PCB’s) to assess whether or not the surface water is meeting the beneficial use of aquatic consumption. Additional stream reaches within the watershed may also be sampled and analyzed, such as collecting trout for mercury testing in coldwater reaches. Mercury and PCB analysis will be conducted on fish tissue. Top carnivore species are particularly important for mercury analysis while rough fish species are important for PCB analysis. Species preferences for top carnivores are:  walleye, northern pike, smallmouth bass, channel catfish, and bluegill. Species preferences for rough fish are:  common carp, redhorse sucker, and white sucker. It is important to collect an appropriate age/length range of these individuals, preferably of edible size. In general as the age/length increases so do the concentrations of these contaminants. An adequate distribution of size classes is critical to characterize or assess the contamination level of these parameters.

Sampling plan

For more details about sampling plans, visit the Watershed approach to restoring and protecting water quality webpage.