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Supplemental Module: Monitoring and Assessment

This module covers the role of monitoring and assessment in the implementation of clean water programs, including reporting on the condition of the Nation’s waters and meeting the fishable/swimmable goals of the Clean Water Act.

Water quality monitoring should be the scientific foundation for the implementation of Clean Water Act programs. Monitoring supports States/Tribes in developing and refining water quality standards, reporting on water quality conditions, listing impaired waters, issuing and enforcing discharge permits, managing nonpoint sources, protecting good quality waters, setting priorities for water quality management, tracking changes in water quality over time, and evaluating the effectiveness of restoration and protection actions. The Clean Water Act assumes monitoring is fundamental to all CWA programs, and makes an adequate State/Tribal water monitoring program a prerequisite for receiving Section 106 grants for administering water pollution control programs.

This module provides basic information on the following:
  • Why is an integrated monitoring program that includes different monitoring designs needed to support multiple clean water programs?
  • What are the critical elements of a monitoring and assessment program?
  • What resources are available?

At the end of the module is a brief quiz intended to touch on aspects of water quality monitoring and assessment. The topic is further examined in the classroom session of this module.

This module's main pages and brief quiz at the end take about 25 minutes to complete. 

On this page:

Importance of an Integrated Monitoring Program

Under the Clean Water Act, States, Tribes, and Territories have the primary responsibility for monitoring and assessing their waters and reporting on water quality. Long-standing critiques by the Governmental Accountability Office, National Research Council, National Academy of Public Administration, and other independent organizations have found that the Nation and the States/Tribes do not have all the monitoring data needed to effectively manage their water programs. Different monitoring approaches are necessary to make scientifically defensible statements about the condition of waters, track changes, and manage water quality protection and restoration at multiple geographic scales.

Under traditional monitoring approaches, States/Tribes have assessed approximately 20 percent of their streams and rivers, 40 percent of lakes, and 30 percent of bays and estuaries. States/Tribes have generally used a site-specific, targeted monitoring approach because it allows them to focus limited monitoring resources on heavily used or problem waters.

Water quality standards and the methods used to monitor and assess waters vary across States and Regions. Often indicators, parameters, and sampling procedures vary across States/Tribes, and sometimes within them. Methods to determine the spatial extent of the assessment (e.g., ¼ mile or 25 miles downstream) also vary. While this approach is consistent with the Clean Water Act and may be appropriate for management of State/Tribal waters, it complicates the process of generating a regional and national picture of water quality and addressing water quality concerns affecting regional and interstate waters.

Key Point. States should strive to integrate different monitoring approaches and coordinate monitoring activities across the State/Tribe, Region, and Nation to provide data for as broad a range of clean water programs as possible. 

EPA issues guidance for use by States/Tribes in implementing their monitoring and assessment programs.

Resource. EPA’s Elements of a State Water Monitoring and Assessment Program (March 2003). 

Resource. Additional guidance is available at EPA’s webpage on Monitoring and Assessing Water Quality.

Resource. Visit EPA’s webpage on the Consolidated Assessment and Listing Methodology (CALM)

Learn More. There are a number of provisions in the Clean Water Act that drive State/Tribal water quality monitoring and assessment. Proceed to the Learn More Topic.


In March 2003, EPA issued national guidance, Elements of a State Water Monitoring and Assessment Program, to promote and structure consistency in State/Tribal monitoring programs. The objective is to move toward more scientifically defensible water quality information for State/Tribal water management decisions and for tracking status and trends in water quality at various geographic scales:  national, regional, State/Tribal, sub-state, watershed, and segment level. This module focuses upon these elements:

Good Planning
  • Identify monitoring objectives.
  • Design the monitoring and assessment project.
  • Develop a quality assurance plan.
Careful Implementation
  • Collect and analyze data for appropriate indicators.
  • Manage the data.
  • Interpret data to develop the assessment.
Informed Communication
  • Convey information and results.
  • Evaluate monitoring efforts.
  • Plan improvements.

Key Point. EPA recognizes that many States/Tribes are in the process of establishing a more rigorous approach to water quality monitoring and assessment. EPA’s guidance entitled Elements of a State Water Monitoring and Assessment Program sets a goal of 2014 for these improvements

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Identifying Objectives


The first element for an effective monitoring and assessment program is identification of the monitoring objectives critical in generating data that will serve the States/Tribes’ management decision needs. Monitoring objectives should reflect the decision needs relevant to all types of waters of the United States, including streams, rivers, lakes, the Great Lakes, reservoirs, estuaries, coastal areas, wetlands, and, to the extent possible, groundwater.

Monitoring objectives are broad and answer questions such as:

  • What is the overall quality of waters in the State/Tribe?
    What is the extent to which waters meet the objectives of the Clean Water Act, attain applicable water quality standards, and provide for the protection and propagation of balanced populations of fish, shellfish, and wildlife?
  • To what extent is water quality changing over time?
    Are the waters getting better?
  • What are the problem areas and areas needing protection?
    Do the waters (e.g., a water body, stream, lake, segment of a stream) support their water quality standards? Can the waters be used for recreation, aquatic life support, drinking water sources, and/or fish consumption?
  • What level of protection is needed?
    What level of protection has the State/Tribe established that is being monitored against? Monitoring programs provide the data to conduct triennial reviews of State/Tribe water quality standards, conduct use attainability analyses, develop and adopt revised designated uses and water quality criteria, establish water quality-based effluent limits in NPDES permits, establish total maximum daily loads, and assess which levels of best management practices for nonpoint sources are most appropriate.
  • How effective are clean water projects and programs?
    Monitoring is needed to evaluate the effectiveness of specific projects and overall programs, including but not limited to Section 319 (nonpoint source control), Section 314 (Clean Lakes), Section 303(d) (TMDLs), Section 402 (NPDES permits), water quality standards modifications, compliance programs (Discharge Monitoring Report information), and generally to determine the success of management measures.

It is important to consider the scale for the monitoring objectives. That is, will the assessment apply to the stream reach scale, the watershed scale, the State or Tribal-wide scale? Ideally, the State/Tribe will set up its monitoring and assessment program to support decision-making at multiple scales.

Designing the Project

States/Tribes should select a combination of monitoring designs (e.g., fixed station, intensive and screening-level monitoring, rotating basin, judgmental and statistical survey designs) that will yield credible data to support multiple clean water programs and inform management decisions.

The efficiencies of an integrated design should extend beyond monitoring costs to program costs because the design can help States/Tribes prioritize which water bodies need more immediate attention.

The table presents a selection of monitoring designs that can be used in combination to support management needs.

Monitoring Design Uses
  • Assess WQS attainment for specific segments.
  • Measure localized water quality trends.
  • Identify sources of pollutants to specific waters.
  • Support development of local management measures (TMDL, NPDES permits, nonpoint source best management practices, WQS).
  • Describe proportion of all waters supporting CWA goals, with documented confidence.
  • Measure water quality trends and CWA program effectiveness.
  • Support development of new WQS.
  • Prioritize targeted monitoring.
Modeling and landscape analysis
  • Support development of local management measures (TMDL, NPDES permits, NPS BMPs, WQS).
  • Predict where water quality is likely impaired.
  • Predict water quality trends.
  • Prioritize targeted monitoring.
clip board

Illustration. Using monitoring designs and tools together can streamline monitoring for Integrated Reporting. Proceed to the Illustration.

Resource. Statistical surveys are a cost-effective means of reporting and communicating to decision-makers and the public about the condition of waters without having to sample every river mile, lake and wetland acre, and estuary square mile in the United States. Visit EPA’s website on Aquatic Resource Monitoring: Design and Analysis

Resource. EPA and States are working together to improve the ability to accurately characterize the condition of the nation’s waters and to track progress. The National Aquatic Resource Surveys address critical gaps and provide much-needed assistance to States and Tribes to enhance their monitoring programs consistent with their monitoring strategies. Visit EPA’s website on the National Aquatic Resource Surveys.

Key Point.A Quality Management Plan (QMP) documents how the State/Tribal monitoring program will plan, implement, and assess the effectiveness of its quality assurance and quality control operations. Quality Assurance Project Plans (QAPPs) document the planning, implementation, and assessment procedures for a particular project, as well as any specific quality assurance and quality control activities.

Resource. EPA guidance on developing QMPs and QAPPs, refer to webpage.

These plans should reflect the level of data quality that is appropriate for the specific uses of the data, such as comprehensive assessment and listing of impaired waters, TMDL development, NPDES permit issuance, and NPS effectiveness. Data quality and quantity needs will vary according to the consequences of the resulting water quality decisions.

Under 40 CFR 130.4(b), State/Tribal monitoring programs are to include collection and analysis of physical, chemical, and biological data as well as quality assurance and control programs to ensure the data are scientifically valid. Under 40 CFR 31.45, if a grantee’s project involves environmentally related measurements or data generation, the grantee must develop and implement quality assurance practices consisting of policies, procedures, specifications, standards, and documentation sufficient to produce data of adequate quality to meet project objectives and minimize loss of data due to out‑of‑control conditions or malfunctions.

Resource. For a clearinghouse of information on monitoring methods and procedures, visit the National Environmental Methods Index

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Collecting the Data

The next step includes selecting core and supplemental indicators to assess water quality standards attainment:

  • Collecting data for a core set of indicators for each applicable designated use.
  • Collecting data for supplemental indicators selected according to site-specific or project-specific decision criteria.

Biological monitoring is the best integrator of multiple stressors/pollutants to indicate a problem. Follow-up monitoring and analysis are needed to identify the pollutant(s) causing the impairment. Supplemental indicators are used to determine potential problem areas (e.g., emerging contaminants, pesticides from agricultural production, excess sediments and nutrients from increased development or road construction).

The following table presents examples of core and supplemental indicators for the major designated uses:

Aquatic Life Recreation Drinking Water Fish / Shellfish
  • Biological communities
  • Basic chemistry (e.g., DO, pH)
  • Nutrients
  • Flow
  • Habitat assessment
  • Landscape condition
  • Pathogen indicators (E. coli, enterococci)
  • Nuisance plant growth
  • Nutrients
  • Chlorophyll
  • Flow
  • Landscape condition
  • Trace metals
  • Pathogens
  • Nitrates
  • Salinity
  • Sediments/TDS
  • Flow
  • Landscape condition
  • Pathogens
  • Mercury
  • Chlordane
  • DDT
  • PCBs
  • Landscape condition
  • Ambient toxicity
  • Sediment toxicity
  • Other chemicals of concern in water or sediment
  • Health of organisms
  • Other chemicals of concern in water or sediment
  • Hazardous chemicals
  • Aesthetics
  • Other chemicals of concern in water or sediment
  • VOCs (in reservoirs)
  • Hydrophyllic pesticides
  • Algae
  • Other chemicals of concern in water or sediment

Resource. Over the years, local volunteers have become increasingly involved in monitoring efforts. Data collected by volunteers may provide valuable information that can be used, for instance, to supplement State/Tribal monitoring data. (Data provided by volunteers is sometimes considered “secondary data,” in contrast to “primary data” collected by the State or Tribe itself.) For relevant considerations, visit EPA guidance document The Volunteer Monitor’s Guide to QAPPs. Visit EPA’s webpage on Volunteer Monitoring,

Learn More. Who else besides State and Tribes monitor water quality? Proceed to the Learn More Topic.

Managing the Data

Monitoring data should be maintained through an accessible electronic database that will allow it to be permanently available and shared among water quality management agencies and others interested in water quality protection and restoration.

STORET is the Agency’s main repository of water quality monitoring data, containing information from across the country submitted by entities that range from small volunteer watershed groups to State and Federal environmental agencies.

  • EPA has released a web-enabled data management/submission framework—the Water Quality Exchange (WQX)—that can be used to submit raw water quality data (as opposed to assessment conclusions) across the web to EPA’s STORET web-based system (STOrage and RETrieval system). Use of the system’s data management/submission tools are provided by EPA at no cost to the user. Many States and other entities involved in water quality monitoring use STORET to manage and share water quality data. A users’ tool is also available for small groups with templates for standard data elements.

Key Point. All States/Tribes should submit water quality data to the STORET warehouse through WQX or WQX-web. States that do not currently use the WQX/STORET system should plan to do so.

Resource. To access STORET, go to the data warehouse’s homepage, which provides comprehensive information on using the system.

Resource. For more information specifically about the Water Quality Exchange, go to What is WQX?

In addition, when submitting data EPA asks that States/Tribes define the geographic location of assessment units using the National Hydrography Dataset (NHD). Providing geographic information supports data analysis and interpretation. The NHD is used for mapping waters for 305(b) water quality inventory reports and for 303(d) lists of impaired waters.

Resource. For more information about the National Hydrography Dataset, visit the U.S. Geological Survey’s webpage on the NHD. Exit Visit 1998 Content Standard for Digital Geospatial Metadata. Exit

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Interpreting the Data

guy fishing with net

Each State/Tribe should have a methodology for assessing attainment of water quality standards based on analysis of various types of data (chemical, physical, biological, land use) from various sources for all waterbody types and all State/Tribal waters.

The methodology should describe how existing and available data and information, relevant to applicable water quality standards and core and supplemental indicators, will be compiled and analyzed to make attainment decisions. The methodology should also describe how the State/Tribe will integrate its primary data—collected specifically for making attainment decisions according to a QAPP—with data from secondary sources, which are collected for a variety of purposes under a variety of quality control practices. (Secondary data could include, for example, volunteer monitoring data or discharge monitoring reports.) The methodology also should:

  • Identify the required or likely sources of existing and available data and information and procedures for collecting or assembling it.
  • Describe or reference requirements relating to data quality and representativeness, such as analytical precision, temporal and geographical representation, and metadata documentation needs.
  • Include or reference procedures for evaluating the quality of datasets.
  • Explain data reduction procedures (e.g., statistical analyses) appropriate for comparing data to applicable water quality standards.

Key Point. The assessment methodology is critical for documenting the hierarchy of indicators, methods, and tools used to assess water quality. It establishes a record and provides for consistency from one reporting period to the next.

Resource. For more information on collecting and using water quality data and developing assessment methodologies, visit EPA’s webpage on the Consolidated Assessment and Listing Methodology (CALM).

Resource. Visit EPA’s website on Aquatic Resource Monitoring.

Conveying Results

The CWA requires that States/Tribes report to EPA on a regular basis about the status of water quality in their respective jurisdictions. The State/Tribe’s monitoring and assessment program should be designed to provide the information needed to comply with these requirements. Key reporting requirements are:

  • Section 305(b) water quality inventory report.
  • Section 303(d) list identifying all impaired waters.

EPA encourages States/Tribes to provide their 305(b) and 303(d) submissions as an “integrated report.” Using the Integrated Report option to submit this information every 2 years satisfies the requirements for both of these sections of the CWA. The submission must be made by April 1 of all even-numbered years.

States report their assessment findings to EPA via the Assessment Database that allows EPA to summarize the States’ water quality and report to Congress and the public.

Resources. For more on reporting requirements for Section 303(d) lists, visi the Supplemental Topics Module of this online training on Listing Impaired Waters for Section 303(d) lists and Developing TMDLs. For more on the Integrated Report, including the recommended reporting format, visit EPA memo on Information Concerning 2010 Clean Water Act Sections 303(d), 305(b), and 314 Integrated Reporting and Listing Decisions.

Key Point. It is also important that States/Tribes convey information on water quality to the public and other stakeholders. Depending on a particular audience’s interest, formats and media to consider can include technical reports, brochures, posters, oral presentations, newspaper articles, and web postings

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Evaluating and Improving

The State/Tribe should periodically evaluate its overall monitoring program as part of a continuous improvement feedback loop. Program evaluation should involve identifying current and future monitoring resources needed to develop as comprehensive and integrated a monitoring program as possible.

Water quality monitoring programs are effective only when they meet the information needs of water quality resource managers. Thus, the State/Tribe’s periodic evaluation process should involve:

  • Determining if the needs of water program managers are being met.
  • Planning for monitoring that may be needed in the future.

Evaluations could include, for example, undertaking audits of the monitoring program, quality assurance protocols, laboratory procedures, and data assessment procedures. Assessments should also take into account needs regarding funding, staff, training, laboratory resources, and upcoming improvements.


  • To help promote consistency in monitoring and assessment approaches, EPA issues guidance for use by States/Tribes in implementing programs that include key elements and established methods.
  • EPA’s recommended framework for water quality monitoring and assessment emphasizes developing a monitoring strategy that includes: clear objectives; multiple and integrated designs for cost-effective data gathering; data collection, management, and analyses with quality assurance plans; informed communication; and a process for evaluating and improving the State/Tribal monitoring program.
  • The State/Tribe’s monitoring and assessment program should provide the information needed to comply with reporting requirements under the CWA. Similarly, the program should support communication with the public and other stakeholders.

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To complete your review of the topic in this module, please take the following brief quiz.

A note about the quiz:  Your answers will NOT be scored or recorded. However, selecting the Submit button for each question will provide you with the correct answers on screen.

Answer each of the questions

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Disclaimer: This online course presentation and any associated links have been prepared by EPA staff for informational purposes only. Their sole purpose is to make available training online from recent Water Quality Standards Academy classroom courses. As such, this online course and any associated links are not binding on EPA or the public and have no legal effect. They do not constitute an EPA statute, regulation or other requirement and do not substitute for such authorities. In addition, the course and any associated links have not been reviewed or endorsed by EPA management. Thus, they are not intended or written as official statements of EPA's scientific views, policies, guidance, or requirements and cannot be used or cited as evidence of EPA's position on any matter.