Water Protection Program fact sheet
Division of Environmental Quality Director: Kyra Moore

This fact sheet outlines and clarifies how Missouri facilities might be affected by recent changes to Section 316(b) of the Clean Water Act, which requires National Pollutant Discharge Elimination System (NPDES) permits to ensure the location, design, construction and capacity of cooling water intake structures reflect the best technology available to minimize harmful environmental impacts associated with the use of these structures. Over half of all water withdrawn each year from waters of the United States is for cooling purposes. By far, the largest industrial use of cooling water is for thermoelectric generation.

Section 316(b) of the Clean Water Act accords the U.S. Environmental Protection Agency broad authority to protect waters of the U.S. from adverse environmental impacts associated with cooling water intake structures, including adverse effects to federally-listed threatened and endangered species and designated critical habitat. Section 7 of the Endangered Species Act (1973) requires federal agencies to consult with the U.S. Fish and Wildlife Service to make certain actions they fund, authorize or carry out do not jeopardize the continued existence of a listed species and do not destroy or adversely modify designated critical habitat. A planning tool is available online to find out which species or critical habitat under Fish and Wildlife Service jurisdiction may be present in your area.

The ruling in 2014 established best technology available standards to reduce impingement and entrainment of fish and shellfish at existing facilities that are designed to intake more than 2 million gallons per day (MGD) of water and use at least 25% of their intake exclusively for dissipating waste heat from industrial processes. The finalized requirements are included in the NPDES permit regulations, which can be found in 40 CFR 122 and 125 Subparts I, J and N. Because Missouri is not concerned with offshore facilities, and the number of new facilities will be minimal, this document discusses only Subpart J of Section 125 (§125.)

Nothing in this ruling authorizes the take of threatened or endangered species of fish or wildlife. Such take is prohibited under the ESA unless it is exempted pursuant to 16 U.S.C. 1536(o) or permitted according to 16 U.S.C. 1539(a). Once the Missouri Department of Natural Resources receives all applicable permit application materials, the department is required to transmit them to the appropriate Fish and Wildlife Service field office for a 60-day review to make sure listed species have been accurately identified as present and to review the measures proposed to reduce adverse environmental impacts.

Definitions and Acronyms

  • Actual Intake Flow: the average volume of water withdrawn annually by cooling water intake structure over the past three years (increases to the past five years after Oct. 14, 2019). This includes days of zero flow and excludes flows used for emergencies or fires. [§125.92(a)]
  • All life stages of fish and shellfish: includes eggs, larvae, juveniles and adults, but does not include barnacles, green mussels, zebra mussels or other specified nuisance species. [§125.92(b)]
  • Best Technology Available: as used in this document and the 316(b) rule, means the best technology available for minimizing adverse environmental impacts.
  • Closed-cycle Recirculating System: a system designed and operated to minimize make-up and blowdown flows withdrawn from a water of the United States for cooling, or a system designed to utilize impoundments constructed before Oct. 14, 2014 that were created to serve as part of the cooling water system. The department may designate a system as being a closed-cycle recirculation system if it adequately demonstrates that water withdrawals specifically for cooling have been minimized. [§125.92(c)]
  • Cooling Water Intake Structure: includes the total physical structure and any associated constructed waterways used to withdraw cooling water from waters of the United States or state. It extends from the point at which water is first withdrawn, up to and including the intake pumps. [§125.92(f)]
  • Entrainment: the intake of all life stages of fish and shellfish through the cooling water intake structure and into the cooling water system; organisms withdrawn into the cooling system. [§125.92(h)]
  • Entrapment: the condition where impingeable fish and shellfish, while not impinged, lack the means to escape. [§125.92(j)]
  • Impingement: the entrapment of all life stages of fish and shellfish against a screen or on the outer part of an intake structure, usually due to flow; organisms pinned against any part of the intake system. [§125.92(n)]

NPDES Permit Requirements and Information

Operators are required to submit basic information such as but not limited to: contact information, facility location and process details, and a list of all permits applied for or received. Most facilities are also required to provide source water data [§122.21(r)(2)], source water baseline biological data [§122.21(r)(4)], cooling water intake structure data [§122.21(r)(3)], cooling water system data [§122.21(r)(5)], and operational status [§122.21(r)(8)]. Specific information can be found in 40 CFR 122.21. In accordance with the 2014 ruling on Clean Water Act §316(b), operators must also submit additional information when applying for NPDES permits. This information is discussed in more detail below.

All Existing Facilities [§122.21(r)(1)(ii)(A)]

In addition to the information previously outlined, applicants for existing facilities must now also submit the following at the time of permit renewal:

  • Identification of protective measures and stabilization activities that have been implemented and how they affect the baseline water condition in the vicinity of the intake [§122.21(r)(4)(x)].
  • A list of fragile species, defined as any fish or shellfish species with an impingement survival rate of less than 30 percent [§122.21(r)(4)(xi)].
  • A description of existing impingement and entrainment technologies at the facility and a summary of their performance [§122.21(r)(5)(iii)].
  • Identification of the chosen method of compliance with impingement mortality standards, along with an impingement technology performance optimization study if required [§122.21(r)(6)].
  • Entrainment performance studies detailing technology efficacy and through-facility entrainment survival for use in determining site-specific best technology available standards for entrainment reduction [§122.21(r)(7)].
  • A report on the operational status of each process unit that uses cooling water [§122.21(r)(8)].
  • All information received from a Fish and Wildlife Service field office [§122.21(r)(1)(ii)(H)].

The department will review all application materials, including any further materials required due to facility size or the construction of new units, and establish best technology available standards for entrainment for each intake on a site-specific basis. Once a final permit establishing entrainment requirements has been issued, the facility must comply with impingement mortality standards and entrainment standards as soon as practicable. The factors considered during this evaluation are described in the Entrainment Best Technology Available Standards section of this document. The department may establish interim compliance milestones for both standards in the permit.

Large-Scale Existing Facilities [§122.21(r)(1)(ii)(B)]

Along with the information required of all existing facilities, large-scale existing facilities (those with an actual intake flow of at least 125 MGD) must also submit:

  • An entrainment characterization study with a minimum of two years of data describing the methods of data collection, the organisms impacted and their characteristics, conclusions, and any supporting calculations [§122.21(r)(9)].
  • Studies that comprehensively detail the technical feasibility of all considered entrainment reduction technologies along with an evaluation of associated costs [§122.21(r)(10)].
  • A study discussing the possible benefits, and estimates of the associated value, of each entrainment reduction technology being considered [§122.21(r)(11)].
  • Studies discussing environmental and other impacts that are not related to water quality for each entrainment reduction technology considered [§122.21(r)(12)].
  • Peer reviews of each report described in this section, carried out by department approved reviewers, accompanied by reviewer information and explanations for significant comments not accepted [§122.21(r)(13)].

New Units at Existing Facilities [§122.21(r)(1)(ii)(D) and (E)]

Applicants for existing facilities with new units must submit the information required of all existing facilities along with identification of the chosen method of compliance with impingement mortality standards for each new unit, along with an impingement technology performance optimization study if required [§122.21(r)(14)].

If the new unit increases the total design intake flow capacity of the existing facility to more than 2 MGD, the applicant must submit all information required of facilities of that size with their permit application. If the new unit increases the total capacity of the existing facility to more than 125 MGD actual intake flow, the applicant must also submit the information required of facilities of that size.

Operational Status Report [§122.21(r)(8)]

A description of the operational status of each process unit that uses cooling water must include:

  • Age of each process unit or line.
  • Any major upgrades completed within the last 15 years
  • Descriptions of any plans for any new units planned within the next five years
  • Descriptions of completed, approved or scheduled upgrades and the Nuclear Regulatory Commission relicensing status of each unit and nuclear facilities.

In addition, power and steam generating units must include capacity utilization rate for the previous five years, describing any extended or unusual outages that might affect flow, impingement, entrainment or other data, and identification of any operating unit that uses less than eight percent of its capacity when averaged over two years. Units not used for power or steam generation must submit seasonal operation data, including any extended or unusual outages that might affect flow, impingement, entrainment or other data, and any plans or schedules for decommissioning or replacing any process units or lines.

Entrainment Performance Study [§122.21(r)(7)]

Any previously conducted studies or studies obtained from other facilities addressing technology efficacy, through-facility entrainment survival, and other aspects of entrainment must be submitted as part of the permit application, along with a description of each study, its underlying data, and a summary of conclusions and results. In the case of studies more than 10 years old or those obtained from other facilities, the application must include an explanation as to why the data is relevant.

Entrainment Characterization Study [§122.21(r)(9)]

Entrainment characterization studies must include at least two years of data, collected during typical operational conditions, representative of the entrainment at the cooling water intake structure. The conditions and frequency of data collection must be identified along with the methods for data collection and analysis. The data must include the following:

  • Taxonomic descriptions of all fish and shellfish species and any species protected by law that are susceptible to entrainment at the intakes.
  • A characterization of each species identified above, including abundance and any fluctuations in distribution based on climate, season, time of day or other behaviors.
  • Documentation of the current entrainment of all life stages of fish, shellfish and protected species.
  • The methods used to account for latent mortality.
  • All assumptions and calculations used to determine total entrainment.

Comprehensive Technical Feasibility and Cost Evaluation Study [§122.21(r)(10)]

The comprehensive technical feasibility and cost evaluation study must be evaluated for each potential entrainment control technology, and can be broken into two portions. The department reserves the ability to require evaluations of entrainment control technologies not identified as candidates by the applicant.

Technical Feasibility

An evaluation of the technical feasibility of closed-cycle recirculating systems, a screen with a mesh size of 2 mm or less, and either water reuse or alternate cooling water sources must be submitted, along with the following:

  • Descriptions of all technologies considered, including alternative designs of closed-cycle recirculating systems.
  • Discussion of land availability, including any candidate areas potentially available upon retiring units or buildings, or after repurposing.
  • Discussion of available sources of water of appropriate quality and quantity to be repurposed for cooling water.
  • Documentation of factors other than cost that might render a potential technology impractical or infeasible.

Cost Evaluation

The cost evaluation includes engineering cost estimates of all entrainment control technologies considered, discussed separately as compliance and social costs, along with any supporting documentation.

Compliance costs include the costs of the permit application; any costs associated with construction and operation of each technology along with any facility modifications necessary to support such construction and operation; those associated with any additional construction or operation permits; and a discussion of the costs and explanation for all reasonable attempts to mitigate detrimental effects identified in the non-water quality environmental and other impacts study.

Social costs are those imposed on the economy as society reallocates resources away from other production activities to attempt to balance the value of the goods and services lost as a facility complies with permit requirements.

Benefits Valuation Study [§122.21(r)(11)]

This study evaluates the benefits of each potential entrainment control technology in one or more of three ways: a qualitative discussion of environmental effects, a quantified analysis expressed in physical or biological units, and a monetized benefits analysis in which dollar values are applied to the quantified analysis. When possible, benefits should be quantified and monetized. The benefits valuation study must include:

  • Any changes in the numbers of individual fish and shellfish lost due to impingement mortality and entrainment, for all life stages of each susceptible species.
  • Estimates for any changes in the stock size or harvest levels of commercial and recreational fish or shellfish species or forage fish species.
  • Description of the basis for any monetized values assigned to changes in the stock size or harvest levels described above, and to any other ecosystem or non-use benefits.
  • A discussion of mitigation efforts completed before Oct. 14, 2014 including how long they’ve been in effect and how effective they’ve been.
  • A discussion of any benefits expected from reductions in thermal discharges from entrainment technologies.
  • A discussion of any other benefits expected to accrue to the environment and local communities.

Non-Water Quality Environmental and Other Impacts Study [§122.21(r)(12)]

This study entails a detailed site-specific discussion of any changes in non-water quality environmental impacts and other impacts as attributed to each potential entrainment control technology. It must include the following:

  • Estimates of changes in energy consumption, noise, air pollutant emissions, and human health and environmental impacts associated with air pollutant emissions.
  • Discussions of facility reliability and impacts to safety.
  • Significant changes in water consumption, including a site-specific comparison of evaporative losses of both once-through cooling and closed-cycle recirculating systems, and documentation of impacts attributable to such changes.
  • A discussion of all reasonable attempts to mitigate each of these factors as identified in the study.

Peer Review [§122.21(r)(13)]

Each study from sections 122.21(r)(10) through 122.21(r)(12) must be submitted to a peer for review. The review of the reports must also be submitted with the application materials.

Entrainment Best Technology Available Standards [§125.98(f)]

After reviewing all of the application information, the department must establish site-specific best technology available standards for entrainment controls that reflect the maximum reduction in entrainment after considering the factors below:

  • Numbers and types of organisms entrained, especially federally or state-listed threatened and endangered species, and designated critical habitat.
  • Impact of changes in particulate emissions or other pollutants.
  • Land availability as it relates to the feasibility of entrainment technology.
  • Remaining useful plant life.
  • Quantified and qualitative social benefits and costs.
  • Thermal discharge impacts.
  • Impacts on the reliability of energy delivery to the immediate area.
  • Impacts on water consumption.
  • Availability of waters other than source water suitable for reuse as cooling water.

The weight given to each factor is to be determined by the department based upon each facility’s circumstances. However, it is the facility’s responsibility to propose each technology considered to the department.

Impingement Mortality Best Technology Available Standards [§125.94(c)]

Existing facilities in Missouri must comply with one of the six technologies listed below, indicating whether for the entire facility or for each cooling water intake structure, submitting the necessary information to demonstrate compliance. Additional requirements to protect shellfish and fragile species may be imposed as necessary.

  • Operation of closed-cycle recirculating systems – by definition: withdrawing new source water to replenish losses due to blowdown, drift and evaporation only – including daily monitoring of actual intake flow representative of normal operating conditions.
  • Operation of a cooling water intake structure with maximum through-screen design velocity of 0.5 feet per second (fps) during all conditions, measured daily.
  • Operation of a cooling water intake structure with a maximum through-screen actual velocity of 0.5 fps during all conditions, measured daily. If the intake lacks a screen, the maximum intake velocity must not exceed 0.5 fps when the source water is at its lowest ambient elevation.
  • Operation of modified traveling screens determined to be the best technology available upon demonstration of their optimization to minimize impingement mortality according to §122.21(r)(6)(i).
  • Adoption of a system of technologies, management practices, and operational measures determined to be the best technology available upon demonstration that the system is optimized to minimize impingement mortality according to §122.21(r)(6)(ii).
  • Achievement of a 12-month impingement mortality performance standard of 24 percent or less for all life stages of fish and shellfish held for a period of 18 to 96 hours.

Impingement Technology Performance Optimization Studies [§122.21(r)(6)(i) and (ii)]

If the chosen method for reducing impingement mortality is either the operation of modified traveling screens [§125.94(c)(5)] or the adoption of a system of technologies [§125.94(c)(6)], the applicant must also submit a study demonstrating that the compliance method has been optimized to best reduce impingement mortality. The use of modified traveling screens need only be supported by an impingement mortality study. For facilities employing a system of technologies, the performance optimization study must include an impingement mortality study, data on rate of impingement, flow reduction data, a total system performance evaluation, and must document how and to what extent each element of the system contributes to its overall performance. Impingement technology performance optimization studies must also describe the data collection approaches used.

Impingement Mortality Study

Impingement mortality studies must include, at minimum, the following:

  • Two years of monthly collected data.
  • A taxonomic description of all organisms collected to the most specific degree possible.
  • Data representing both impingement and mortality due to impingement, and a description of how the location of the cooling water intake structure is accounted for in these measurements.
  • How the mortality of organisms naturally near death was accounted for.
  • How mortality due to holding times was accounted for.
  • Entrapment represented as impingement mortality, if the facility entraps fish or shellfish.
  • Percent impingement mortality reflecting optimized operation.

Rate of Impingement

If impingement mortality is reduced in part by a decrease in impingement, the applicant must provide an estimate of how the rate of impingement is credited towards reduced impingement mortality along with any supporting documentation. The estimated rate of reductions must be based on a comparison to a once-through cooling system with a traveling screen having a withdrawal point at the shoreline of its source water body. Data must be collected, at a minimum, on a monthly basis for two years.

Flow Reduction

If impingement mortality is reduced in part by flow reductions, the applicant must document how this flow reduction results in impingement reductions, and in turn how reduced impingement results in reduced impingement mortality. This must be supported by two years of daily intake flow data and a description of the extent to which flow reductions are seasonal or intermittent.

Total System Performance

Facilities employing a system of technologies, operational measures, or management practices must document the percent impingement mortality reflection optimized operation and all supporting calculations. Total system performance is the combination of impingement mortality performance reflected by the impingement mortality study, rate of impingement data, and flow reduction data.

Monitoring and Reporting [§125.96 and §125.97]

Several of the impingement standards have specific monitoring requirements, whereas the monitoring requirements for entrainment will be determined on a site-specific basis. Inspections to make sure any technologies required for compliance are being appropriately operated and maintained must be conducted weekly, either visually or via remote monitoring devices.  Additional monitoring may be required, especially where the department has determined additional measures are necessary to protect federally-listed species.

As part of the monitoring requirements, the owner or operator of any existing facility must submit the following information to the department:

  • Discharge Monitoring Reports (DMRs) and the results of all monitoring, demonstrations, and any other information required by the permit in order to determine compliance with the permit conditions and requirements.
  • Any status reports required by the department.
  • An annual certification statement and report consisting of a statement that the previous year’s annual certification is still pertinent along with any applicable data, or if cooling water withdrawals or operation has been substantially modified, these changes must be summarized in the report before being signed by the responsible officer.

Reports including results of any required monitoring will be submitted yearly at a minimum, or otherwise according to the schedule established in the permit. Records of all report submissions must be retained until the subsequent permit is issued. All records supporting the department’s determination of best technology available for entrainment must be retained until the department revises the determination of best technology available for entrainment in the permit.

Alternative Requirements

Applicants have the ability to request alternative schedules or requirements where applicable. When the applicant requests an alternative or exemption, the burden lies with the applicant to demonstrate the need for the alternative or exemption. The Department is authorized to request additional information as well as impose additional requirements or conditions as necessary.

Reduced Requirements

  • In the case of permit proceedings begun before Oct. 14, 2014, if the department deems the submitted information adequate, best technology available standards for impingement mortality and entrainment may be determined without any further information. [§125.98(g)].
  • Any facilities to be retired before their current permit expires are not required to submit any of the newly added information required for permit applications. [§122.21(r)(1)(ii)(F)].
  • Any facilities to be retired after their current permit expires but within one permit cycle may have a significant portion of the newly added application information waived, but must still identify the chosen method of compliance with the impingement mortality standard and also submit an operational status report. [§122.21(r)(1)(ii)(G)].
  • After the initial submission of all required information under §122.21(r), the applicant can request to reduce the information required in future permit applications upon demonstration that the facility and water body conditions remain substantially unchanged. This request must be submitted at least two years and six months prior to the expiration of the effective permit. [§125.95(c)].
  • Large-scale existing facilities intending to comply with the best technology available standards for entrainment using a closed-cycle recirculating system may have the portion of the application information specific to large-scale facilities reduced or waived by the department. [§122.21(r)(1)(ii)(B)].
  • If the annual average capacity utilization rate of existing power generating units is demonstrated to be less than 8% when averaged over 24 consecutive months, the applicant may request less stringent requirements for impingement mortality for only the qualifying units. [§125.94(c)(12)]

Alternative Schedules and Requirements

  • Any facilities with effective permits expiring on or before July 14, 2018 may request alternative schedules for submitting the application information required in §122.21(r). If an applicant adequately demonstrates that it cannot develop the required material by the applicable date, the department must establish an alternate schedule. [§125.95(a)(2)].
  • Applicants at existing facilities with new units can seek alternate requirements allowing for the employment of technologies and operational measures that are shown to reduce the adverse environmental impacts of cooling water intake structure by at least 90% of the reduction that could be achieved if the facility used closed-cycle recirculating system. [§122.21(r)(1)(ii)(D) and (E)].
  • For new units at existing facilities, if the compliance costs for each new unit would be wholly out of proportion to those costs considered by the EPA in establishing the requirements, or if compliance would result in significant adverse impacts to energy markets, air quality or water resources aside from entrainment and impingement, any supporting documentation must be submitted in pursuit of reduced compliance requirements.
  • Upon review of the application information, the department may determine that the rates of impingement at a certain facility may be so low that additional impingement controls aren’t necessary. [§125.94(c)(11)].
  • If the intake for an existing facility is located in a manmade lake or reservoir and the fisheries are stocked and managed by a state or federal natural resource agency, the department may waive some or all of the permit application information required of facilities with cooling water intake structures. If the lake or reservoir in question is a designated critical habitat or if it contains federally or state–listed threatened or endangered species, no exemptions will be granted. [§125.95(a)(3)].
  • If compliance for any nuclear facilities conflicts with the safety requirements established by the Nuclear Regulatory Commission, the department will determine best technology available standards for minimizing adverse environmental impact that do not conflict with those safety requirements. [§125.94(f)].


This flowchart provides a rough framework to help evaluate which requirements apply to the various types of facilities. This does not account for any exemptions or inclusions which may be required by the department.


Nothing in this document may be used to implement any enforcement action or levy any penalty unless promulgated by rule under chapter 536 or authorized by statute.

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