Recommendations and guidance for utilizing stream monitoring to meet TMDL permit requirements
Recommendations and guidance for utilizing stream monitoring to meet TMDL permit requirements

Biological monitoring in a stream. Biological impairments are often associated with excess TSS. Photo courtesy of MPCA's Flickr site.

The primary reasons for a permittee to perform monitoring of receiving waters are to (a) evaluate the impact of TMDL implementation strategies enacted throughout the watershed, and (b) evaluate impairment status to determine if the impaired waterbody can be removed (i.e., delisted) from the 303(d) Impaired Waters List. The following subsections outline the basics of developing a monitoring program to meet goals established within the Guidance Manual for Assessing Quality of Minnesota Surface Waters for Determination of Impairment: 305(b) Report and 303(d) List (MPCA, 2018a), and developing a monitoring protocol standard operating procedure (SOP). Specifically, the Establishing a Monitoring Program section provides guidance on when, where, and what to sample, while the Establishing a Monitoring Protocol section provides guidance on how to sample (i.e., sampling SOP).

Establishing a Monitoring Program

Before developing or implementing a lake or stream monitoring program, the applicable TMDL(s) should be reviewed to determine (a) if an ongoing water quality monitoring program exists or will be implemented and (b) what organization(s) are responsible for water quality monitoring (e.g., individual permitteess, the applicable Watershed District or Watershed Management Organization (WMO), etc.). Review of ongoing and planned water quality monitoring programs can help a permittee optimize sampling procedures to supplement ongoing monitoring efforts and help identify potential partnering opportunities with other organizations (e.g., WDs, WMOs, Citizen-Assisted Monitoring Program (CAMP), Soil and Water Conservation Districts (SWCDs), Metropolitan Council, etc.). To encourage statewide water quality monitoring efforts, the MPCA offers Surface Water Assessment Grants (SWAG) to eligible partners, including MS4s. More information on SWAG requirements and grant application can be found on the MPCA’s Surface Water Assessment Grants webpage.

In addition to review of planned or ongoing monitoring programs, the applicable TMDL(s) should be reviewed to determine the specific water quality standard(s) that apply to the impaired waterbody. Water quality standards applicable to the impaired waterbody are specific to the pollutant (e.g., chloride), the water body type (e.g., lake), and the water use classification (e.g., Class 2A).

Monitoring requirements: streams

The following subsections outline specific stream monitoring program requirements related to each of the four (4) pollutants discussed on this page: total suspended solids (TSS), total phosphorus (TP), bacteria, and chloride.

Total suspended solids (TSS)

Based on review of TSS water quality standards within the Minnesota Rule, Chapter 7050 (MINN. R. 7050, 2018), for many use classifications (e.g., Class 2A) and ecoregions (e.g., North River Nutrient Region), TSS standards are structured as follows.

TSS standards for [use classification, e.g., Class 2A] may be exceeded for no more than ten percent of the time. This standard applies April 1 through September 30.

The above standard, which supersedes the previous standard for turbidity, is the most common form of TSS standard within the Minnesota Rules (MINN. R. 7050, 2018), but the TSS standard may vary based on the use classification and ecoregion (e.g., Lower Mississippi River mainstem TSS standards are based on 50 percent exceedance from June 1 through September 30). For this reason, it is critical to review the applicable TMDL(s) to determine what water quality standard(s) apply to the impaired waterbody. Based on the most-common form of TSS standard and specific impairment assessment and delisting requirements for TSS, the following list outlines specific recommendations related to the development of a stream TSS monitoring program. Link here to specific monitoring protocol recommendations.

TSS Monitoring Program Recommendations

Number of samples per year:
- Minimum: twenty (20) observations in the most recent 10 years, and at least 10 in the last 5 years.
- Recommended: at least five (5) samples collected per year between April 1 and September 30. Sampling dates should be selected and fixed before the monitoring season to remove sampling bias in selected monitoring dates. Monitoring should, to the extent possible, be collected at intervals throughout the period of April 1 to September 30 (i.e., sampling should capture seasonal changes in water quality).
Seasonal monitoring recommendations: Samples must be collected between April 1 and September 30 of the sampling year unless the applicable water quality standard specifies a different period for standard compliance (e.g., TSS standards based on summer average values must be collected between June 1 and September 30 of the monitoring year).
Flow monitoring recommendations: because TSS concentrations can vary based on flow rate, monitoring should ideally reflect a variety of flow conditions. For this reason, dry-weather monitoring, post-rainfall sampling, and seasonal sampling should be considered to ensure a variety of flow rates are captured in the TSS monitoring dataset.
Sampling location(s): Selected sampling locations should be consistent with sampling locations used to originally define impairment. Sampling locations used to define impairment may be outlined within the applicable TMDL(s). If not, contact MPCA to determine sampling locations used to define impairment.
Sampling protocol (i.e., sample collection guidance): link here

Eutrophication standard: streams (TP, chlorophyll-a, and Secchi disk transparency)

Intersection of two impaired streams; TSS on the left and phosphorus (eutrophication) on the right. Photo courtesy of MPCA's Flickr site.

Stream eutrophication water quality standards established in Minnesota Rule, Chapter 7050 (MINN. R. 7050, 2018) require paired observations of TP, chlorophyll-a, five-day biological oxygen demand (BOD5) and diel dissolved oxygen (DO) flux. From Part 7050.0222, Subp. 3b:

Eutrophication standards for rivers, streams, and navigational pools are compared to summer-average data or as specified in subpart 3. Exceedance of the total phosphorus levels and chlorophyll-a (seston), five-day biochemical oxygen demand (BOD5), diel dissolved oxygen flux, or pH levels is required to indicate a polluted condition.

The standard requires paired observations of TP, chlorophyll-a, BOD5, and diel DO flux during the summer period (June 1 through September 30) of the monitoring year. As outlined in Part 7050.0222, Subp. 3, standards for each of the four (4) parameters used to evaluate stream eutrophication vary by use classification (e.g., Class 2B) and ecoregion (e.g., North Central Hardwood Forests). The applicable water quality standards for the impaired waterbody will be outlined in the applicable TMDL report.

Based on Minnesota stream eutrophication standards and specific impairment assessment and delisting requirements for stream eutrophication, the following list outlines specific recommendations related to the development of a stream eutrophication monitoring program. Link here for specific monitoring protocol recommendations.

Stream Eutrophication Monitoring Program Recommendations

Monitored parameters:
- Minimum: total phosphorus (TP) and the response variable(s) that were originally used to define stream impairment.
- Recommended: total phosphorus (TP) and all stream eutrophication response variables: chlorophyll-a, BOD5, diel DO flux, and pH.
Number of samples:
- Minimum: twelve (12) paired samples over a minimum of 2 years for TP, chlorophyll-a, and BOD5 twenty (20) samples of pH over a minimum of 2 years, and two (2) four-day DO sonde deployments to evaluate diel DO flux.
- Recommended: twenty (20) paired samples of TP, chlorophyll-a, and BOD5 per year during the summer period of June 1 through September 30 (i.e., 5 per month), twenty (20) samples of pH over a minimum of 2 years during the summery period, and two (2) four-day DO sonde deployments per year during the summer period.
Seasonal monitoring requirements: Samples must be collected during the summer period (June 1 and September 30) of the sampling year.
Sampling location(s): Selected sampling locations should be consistent with sampling locations used to originally define impairment. Sampling locations used to define impairment may be outlined within the applicable TMDL(s). If not, contact MPCA to determine sampling location(s) used to define impairment.
Sampling protocol (i.e., sample collection guidance): link here

Bacteria (E. coli)

Based on review of bacteria (E. coli) water quality standards within Minnesota Rule, Chapter 7050 (MINN. R. 7050, 2018), for many use classifications (e.g., Class 2A) and ecoregions (e.g., North River Nutrient Region), E. coli standards are structured as follows.

From Part 7050.0222, Subp. 2 (Class 2A): “Escherichia (E.) coli bacteria shall not exceed 126 organisms per 100 milliliters as a geometric mean of not less than five samples representative of conditions within any calendar month, nor shall more than ten percent of all samples taken during any calendar month individually exceed 1,260 organisms per 100 milliliters. The standard applies only between April 1 and October 31.

The above standard, which supersedes the previous standard for fecal coliform bacteria, is the most common form of E. coli standard in Minnesota Rules (MINN. R. 7050, 2018), but the E. coli standard may vary based on the use classification (e.g., for Class 3C water bodies, the geometric mean standard is 630 organisms per 100 milliliters, rather than 126). For this reason, it is critical to review the applicable TMDL(s) to determine what water quality standard(s) apply to the impaired waterbody.

Based on the most-common form of E. coli standard and specific impairment assessment and delisting requirements for E. coli, the following list outlines specific recommendations related to the development of a stream E. coli monitoring program. Link here for specific monitoring protocol recommendations.

Bacteria (E. coli) Monitoring Program Recommendations

Number of samples per year:
- Minimum: fifteen (15) samples over a two-year period in the last 10 years, with a minimum of five (5) samples per month for at least 3 months where the standard applies (i.e., April-October).
- Recommended: five (5) samples per month for the period of April-October (i.e., 35 samples per year), or five (5) samples per month for the critical period of June-September (i.e., 20 samples per year).
Seasonal monitoring recommendations: The standard applies for the period of April 1 to October 31.
Flow monitoring recommendations: Recommended: because E. coli concentrations can vary based on flow rate, monitoring should ideally reflect a variety of flow conditions. For this reason, dry-weather monitoring, post-rainfall sampling and seasonal sampling should be considered to ensure a variety of flow rates are captured in the bacteria monitoring dataset.
Sampling location(s): Selected sampling locations should be consistent with sampling locations used to originally define impairment. Sampling locations used to define impairment may be outlined within the applicable TMDL(s). If not, contact MPCA to determine sampling location used to define impairment.
Sampling protocol (i.e., sample collection guidance): link here

Chloride

Chloride water quality standards within the Minnesota Rule, Chapter 7050 (MINN. R. 7050, 2018) are consistent for all Minnesota waters (i.e., all use classifications). Specifically, Minnesota Rules define a chronic toxicity-based chloride water quality standard of 230 mg/L (i.e., chronic standard), and an acute toxicity standard of 860 mg/L (i.e., maximum standard). Specific data requirements for evaluation of impairment condition for both the chronic and maximum chloride water quality standard established in the Guidance Manual for Assessing the Quality of Minnesota Surface Waters for Determination of Impairment: 305(b) Report and 303(d) List (MPCA, 2014) are outlined, below.

Chronic standard (230 mg/L):
- Exceedances of chronic standards for toxic pollutants are evaluated over a consecutive three year period.
- Two or more exceedances of the chronic standard in three years is considered an impairment.
- Chronic water quality standards are defined as a four day (4-day) average concentration. If concentrations in the waterbody are relatively constant, a single sample concentration value may be used to define the 4-day average. When concentrations are more variable, multiple samples or time-weighted composite samples are necessary to calculate an accurate average concentration.
Maximum standard (860 mg/L):
- Exceedances of the maximum standards for toxic pollutants are evaluated over a consecutive three year period.
- One (1) exceedance of the maximum standard is considered an impairment.

The MPCA has published several Statewide Chloride Resources, including the Draft Statewide Chloride Management Plan (MPCA, 2019) and specific protocols related to stream and lake chloride monitoring.

Based on review of chloride standards, statewide guidance documents, and specific impairment assessment and delisting requirements for chloride impairment, the following list outlines specific recommendations for developing a stream chloride monitoring program. Specific monitoring protocol recommendations are discussed here.

Chloride Monitoring Program Recommendations

Number of samples per year:
- Minimum: five (5) samples over any 3-year interval in the past 10-years.
- Recommended: five (5) samples per year for a 3-year interval. If chloride concentration show high daily-variability, 4-day average sampling is required (i.e., five (5) separate 4-day average chloride concentrations should be used to evaluate chronic impairment).
Location and depth of monitoring: Recommended: samples should be taken mid-stream, mid-depth whenever possible.
Monitoring and flow rate: Recommended: because chloride concentrations can vary based on flow rate, monitoring should ideally reflect a variety of flow conditions. For this reason, dry-weather monitoring, post-rainfall sampling, and seasonal sampling should be considered to ensure a variety of flow rates are captured in the chloride monitoring dataset.
Seasonal / critical period monitoring requirements:
- Recommended: chloride concentration can vary significantly throughout the season due to critical chloride loading periods (e.g., winter deicing efforts). For this reason, the TMDL should be reviewed to determine if a critical period was identified (i.e., a seasonal period of most-elevated chloride concentrations). The following list provides examples of periods of elevated chloride concentration related to land use:
  - December through April for streams in urban areas and locations near deicing practices.
  - April through November for streams downstream of waste water treatment plant (WWTP) discharge locations.
  - April through November for streams downstream of heavy agriculture, near tile drainage systems, and/or proximal to gravel roadways that receive dust management.
Note: streams dominated by baseflow (i.e., groundwater flow) may show elevated chloride concentrations at periods other than those listed above.
Sampling location(s):
- Selected sampling locations should be consistent with sampling locations used to originally define impairment. Sampling locations used to define impairment may be outlined within the applicable TMDL(s). If not, contact MPCA to determine sampling location(s) used to define impairment.
- Note: if there are multiple monitoring locations along the reach, all samples collected at a given depth (see definition of “shallow”, “deep”, and “mid-depth”, above) are combined for the 4-day average calculation.
Miscellaneous recommendations: **Recommended: conduct paired conductivity (i.e., specific conductance) measurements during chloride monitoring. In some cases, a waterbody-specific chloride-conductivity relationship can be established. In these cases, conductivity can serve as a surrogate for chloride (as monitoring conductance is faster and cheaper than monitoring chloride directly). Review the TMDL to determine if a waterbody-specific chloride-conductivity relationship has been established
Sampling protocol (i.e., sample collection guidance): link here

Establishing a Monitoring Protocol

The MPCA has specific requirements and protocols related to water quality data collection, laboratory processing of water quality samples, data processing of laboratory results, and final submittal of water quality data to the MPCA for review. Specifically, the MPCA uses a data processing system called EQuIS (Environmental Quality Information System) to store and process water quality data collected from over 17,000 sampling locations across the state, and requires that data be collected and processed in a manner which is compatible with EQuIS.

There are many publicly available Quality Assurance Project Plan (QAPP) and monitoring Standard Operating Procedure (SOP) documents which can be used as a framework for developing a monitoring protocol. The following subsections provide an overview of EQuIS requirements and a summary of lake and stream monitoring QAPP and SOP documents.

EQuIS

The MPCA has developed extensive guidance related to establishing EQuIS projects, and developed tools and guidance to assist monitoring and laboratory staff to process data in an EQuIS-compatible format. The following steps provide a basic overview of the EQuIS data collection and submittal process: establishing an EQuIS project, processing collected water quality data, and submitting collected data to the MPCA for review. Collecting, processing, and submitting EQuIS data requires contact and coordination with an MPCA EQuIS team member.

Coordinate with an MPCA EQuIS team member and establish an EQuIS project (i.e., submit the EQuIS Project Establishment Form).
Submit a location establishment form.
Collect water quality data and submit to a State-certified laboratory.
1. Procedures to collect water quality samples and submit to a certified laboratory, including pre- and post-monitoring protocols, quality assurance and quality control ( QA/QC), and guidance regarding chain of custody (COC) preparation and documentation are discussed below.
2. The MPCA EQuIS team member can be contacted regarding State-certified laboratories.
Submit EQuIS formatted data to the MPCA for review.
1. The EQuIS Data Gathering Engine (EDGE) can be used to generate EQuIS formatted data during field data collection.
2. The Lab_MN lab data storage spreadsheet can be used by certified labs to generate EQuIS formatted data of laboratory results.
3. If not using EDGE or Lab_MN, data can be manually formatted into the Surface Water Data Template.

Monitoring Quality Assurance Program Plan (QAPP)

The primary objective of a QAPP is to define the data quality assurance (QA) goals and procedures applicable to a monitoring program (MCES, 2003). A lake or stream monitoring QAPP must also provide an overview of program design (e.g., program organization, responsibilities, monitoring parameters, sampling locations, etc.), and must define sampling methods (e.g., sampling locations and monitored variables), analytical procedures, QA procedures, and data review protocols.

For this reason, a QAPP document may also contains monitoring SOP(s), defining sampling procedures, field analysis, laboratory analysis, and data review and QAQC measures.

The following subsections provide a summary of monitoring QAPP documents which can be used as templates for developing a lake or stream monitoring QAPP.

MCES Stream Monitoring QAPP

Met Council's Quality Assurance Program Plan for streams defines the data quality assurance goals and the quality assurance procedures that are applicable to Met Council's stream monitoring program.

The Metropolitan Council Environmental Services Quality Assurance Program Plan: Stream Monitoring (MCES, 2003; updated 2011) is a QAPP for the MCES’s Nonpoint Source Pollution Monitoring Program and Watershed Outlet Monitoring Program (WOMP). The QAPP defines goals, objectives, program organization, responsible parties, specific sampling procedures and protocols (e.g. monitoring SOPs, QA procedures, laboratory analytical procedures, etc.), and the monitoring locations, monitored variables, and monitoring frequency for both stream monitoring programs. Specifically, the QAPP is organized into the following sections:

Introduction: defines the background and purpose of the QAPP, as well as the relationship of the QAPP to other guidance documents (specifically, the monitoring SOPs included as appendices).
Program Organization and Responsibility: defines the organization of the QAPP, responsible parties, and defines roles and responsibilities for positions and individual staff members.
Monitoring Program Description: defines the study area, specific monitoring locations, monitored variables (e.g., Total Phosphorus, CBOD 5-day, etc.), and monitoring frequency.
Quality Assurance Objectives: defines QA objectives related to precision, accuracy, representativeness, completeness, comparability, and analytical sensitivity.
Sampling Methods: defines procedures and protocols for two forms of sampling: instantaneous grab sampling and flow-weighted composite sampling. Provides and overview of sampling procedures, field equipment, and bottle preparation, etc. and refers reader to the field sampling SOPs included in the QAPP appendices.
Field and Sample Custody Documentation: defines the field and sample documentation requirements for the MCES stream monitoring programs. Field documentation (e.g., field conditions, time, weather conditions, deviation from written procedures, standardized field documentation sheets) and laboratory chain-of-custody are critical for interpreting results and identifying erroneous samples (e.g., mislabeled samples).
Field Measurement Procedures: defines field monitoring equipment (e.g., specific models of in situ monitoring equipment), monitoring station layout, maintenance, and operations, and a description of all monitoring parameters. More details related to field procedures are included in the monitoring SOPs included in the QAPP appendices.
Laboratory Analytical Procedures: defines the laboratory analytical method for each monitored variable and identifies the State-certified laboratory used for sample processing and analysis. Additional information relate to laboratory procedures, processes, and QA program are included in the laboratory QA manual included in the QAPP appendices.
Quality Assurance Procedures: defines QA procedures relate to data review and validation, QA audits and reporting, and corrective action strategies.
Data Reporting: defines reporting protocols related to automate electronic data reporting and annual assessment reporting.

The organization of the MCES Stream Monitoring QAPP can be used as template for the development of a stream or lake monitoring QAPP. In addition to defining the organization, goals, and QA procedures for the monitoring programs, the QAPP also includes sampling, field analysis, laboratory analysis, and data review SOPs as appendices to the document. The SOPs outline specific monitoring procedures to be followed in the field (e.g., equipment checklist, grab sample bottle and equipment cleaning, field duplicate collection and labeling, health and safety procedures, etc.). Monitoring SOPs are discussed in more detail below.

Other Monitoring QAPP Resources

The MPCA and United States Environmental Protection Agency (USEPA) have developed many guidance documents related to QA and the development of QAPPs. Specific QAPP guidance documents and QA tools are summarized below:

MPCA Quality System: aggregated resources related to QA of environmental data. Includes many QAPP development documents and examples of completed QAPPs. Additionally, includes documents related to the development of SOPs, example SOPs (e.g., lake monitoring SOP), and State-certified laboratory guidance and reference documents.
MPCA QA Project Plan Guidance: guidance document for developing MPCA Remediation Program QAPPs.
EPA QAPP Development Tool: web-based QAPP development tool. The tool provides step-by-step guidance related to developing a surface water monitoring QAPP, and is partitioned into the following six (6) modules:
- Module 1 – guidance on preparing a QAPP.
- Module 2 – QAPP template.
- Module 3 – Model QAPP: provides and model example of a completed QAPP.
- Module 4 – references and links for technical and QA information to assist in developing a QAPP.
- Module 5 – standard operating procedures (SOPs): contains development guidance and example SOPs related to surface water monitoring.
- Module 6 – selecting an environmental laboratory: provides guidance related to selecting a State-certified laboratory for sample processing.
EPA Requirements for QAPPs: defines EPA QAPP requirements.

Questions related to QAPP development, QA procedures, or the references listed above can be directed to any of the MPCA QA coordinators listed in the “Contacts” section of the MPCA Quality System webpage.

Monitoring Standard Operation Procedure (SOP)

As discussed above, a monitoring standard operating procedure (SOP) is a critical component of a complete monitoring QAPP. A monitoring SOP defines specific protocols related to field sample collection and laboratory analysis, and often also includes pre-field protocols (e.g., equipment and supply checklist, pre-field bottle preparation and labeling, etc.), post-sampling protocols (e.g., sample preparation and preservation, sample chain of custody, etc.) and other protocols not specifically related to monitoring and sample collection (e.g., boat and canoe preparation, health and safety, inclement weather protocols, etc.).

The following subsections provide a summary of monitoring SOP documents which can be used as templates for developing a lake or stream monitoring SOP. It is recommended that the documents discussed in this section be used in conjunction with specific monitoring guidance outlined in the applicable TMDL when developing a lake or stream monitoring SOP.

NOTE: See example case studies in which monitoring was used to help identify pollutant sources, evaluate the impact of implementation strategies, and ultimately delist a formerly-impaired water body.

MPCA Lake and Stream Water Quality Sampling SOPs

MPCA's Standard Operating Procedures: Intensive Watershed Monitoring – Lake Water Quality Sampling outlines sampling procedures applicable to all Minnesota lakes

MPCA's Standard Operating Procedures: Intensive Watershed Monitoring – Lake Water Quality Sampling outlines sampling procedures applicable to all Minnesota streams

The Standard Operating Procedures: Intensive Watershed Monitoring – Lake Water Quality Sampling (MPCA, 2018c) and Standard Operation Procedures: Intensive Watershed Monitoring – Stream Water Quality Component (MPCA, 2018d) are SOPs created by the MPCA for local partners contracted through the MPCA’s Surface Water Assessment Grants Program. The SOP outlines sampling procedures applicable to all Minnesota lakes and streams, including pre-sampling requirements, equipment and supply checklists, on-site sampling procedures, QAQC procedures (e.g., field sample duplicates), post-sampling procedures, and a detailed discussion of health and safety protocols. In addition to pre- and post-sampling procedures, the SOP discusses bottle labeling and the chain of custody (COC) procedures for delivering samples to State-certified laboratories, and final data preparation and submittal to EQuIS.

Other Monitoring SOP Resources

The MPCA, USEPA, and MCES have developed many publically available guidance documents related to the development of surface water monitoring SOPs. Specific SOP documents which be used as templates to develop a surface water monitoring SOP are summarized below. It is recommended that the documents discussed in this section be used in conjunction with specific monitoring guidance outlined in the applicable TMDL when developing a lake or stream monitoring SOP:

Chloride Monitoring Guidance for Lakes (MPCA, 2015a) and Chloride Monitoring Guidance for Streams and Stormsewers (MPCA, 2015b): these documents are similar in scope to the MPCA lake and stream monitoring SOPs (MPCA, 2018c; MPCA, 2018d), but include specific guidance related to monitoring chloride, including a detailed winter monitoring SOP. Winter monitoring guidance includes a detailed description of how to predict and monitor winter thaw and rain events, which often produce elevated chloride concentration in streams due to mobilization of deicing salts accumulated over winter deicing operations.
MCES Quality Assurance Program Plan: Stream Monitoring (MCES, 2003; updated 2011): the stream monitoring QAPP contains sampling, field analysis, laboratory analysis, and data review SOPs as appendices.
EPA QAPP Development Tool: Module 5 of the web-based tool contains development guidance and example SOPs related to surface water monitoring. SOP documents can requested from the EPA via the EPA contact listed in Module 5.

Questions related to SOP development can be directed to any of the MPCA QA coordinators listed in the “Contacts” section of the MPCA Quality System webpage.

Related pages

TMDL MS4 permit guidance

TMDL toolkit for MS4 permit compliance

Access a quick guide for using models to meet MS4 TMDL requirements

TMDL guidance and general information

Recommendations and guidance for utilizing stream monitoring to meet TMDL permit requirements Recommendations and guidance for utilizing stream monitoring to meet TMDL permit requirements

Contents