Office of Water

EPA 820-B-14-004

September 2014

Water Quality Standards Handbook

Chapter 5: General Policies

 

 

 

 
Water Quality Standards Handbook 

Chapter 5: General Policies 

 

(40 CFR 131.13)

Table of Contents

Introduction .......................................................................................................................... 1

5.1 Mixing Zones................................................................................................................... 1

5.1.1 Recommended Contents of State and Tribal Mixing Zone Policies......................... 3

5.1.2 Situations in Which Mixing Zones May Not Be Appropriate ................................... 9

5.1.3 Mixing Zones for the Discharge of Dredged or Fill Material.................................. 10

5.1.4 Mixing Zones for Aquaculture Projects ................................................................. 11

5.2 Critical Low Flows for Water Quality Criteria Implementation .................................... 11

5.3 Variances from Water Quality Standards..................................................................... 15
1

Introduction 

As specified in 40 CFR 131.13, states and authorized tribes may, at their discretion, adopt certain 

policies into their water quality standards (WQS) that generally affect how their WQS are applied or 

implemented.

1 Examples of such general policies include those affecting mixing zones, critical low 

flows, and WQS variances. As the regulation indicates, states and tribes are not required to adopt 

general policies. However, if a state or tribe chooses to adopt a general policy, such policies are 

subject to EPA review and approval or disapproval under Section 303(c) of the Clean Water Act 

(CWA) if they constitute new or revised WQS (see Chapter 1 of this Handbook). This chapter 

provides an overview of three types of general WQS policies. In particular, Section 5.1 of this 

chapter discusses mixing zones, Section 5.2 discusses critical low flows, and Section 5.3 discusses 

variances.

5.1 Mixing Zones 

A mixing zone is a limited area or volume of water where initial dilution of a discharge takes place 

and where certain numeric water quality criteria may be exceeded. The CWA does not require that 

all criteria be met at the exact point where pollutants are discharged into a receiving water prior to 

the mixing of such pollutants with the receiving water. Sometimes it is possible to expose aquatic 

organisms to a pollutant concentration above a criterion for a short duration within a limited, 

clearly defined area of a waterbody while still maintaining the designated use of the waterbody as 

a whole. Where this is the case, a state or authorized tribe may find it appropriate to allow ambient

concentrations of a pollutant above the criterion in small areas near point-source outfalls (i.e., 

mixing zones). 

Mixing zones do not constitute new state or tribal criteria or changes to the state- or 

tribe-adopted and EPA-approved criteria. Therefore, the narrative and/or numeric criteria for the 

waterbody are still the applicable criteria within the boundaries of the mixing zone. A mixing zone 

simply authorizes an applicable criterion to be exceeded within a defined area of the waterbody 

while still protecting the designated use of the waterbody as a whole. Since 1983, the guidance in 

this Handbook has described mixing zones as areas where criteria may be exceeded rather than 

areas where criteria do not apply. 

 

1 Throughout this document, the term “states” means the fifty states, the District of Columbia, the 

Commonwealth of Puerto Rico, the Virgin Islands, Guam, American Samoa, and the Commonwealth 

of the Northern Mariana Islands. The term “authorized tribe” or “tribe” means an Indian tribe 

authorized for treatment in a manner similar to a state under CWA Section 518 for purposes of 

Section 303(c) WQS.
2

By authorizing a mixing zone, states and tribes allow some portion of the waterbody to mix with and 

dilute particular wastewater discharges before evaluating whether the waterbody as a whole is 

meeting its criteria. In addition to the WQS regulation at 40 CFR 131.13 described above, the use of 

dilution is supported by the National Pollutant Discharge Elimination System (NPDES) permitting

regulation at 40 CFR 122.44(d)(1)(ii), which requires the permitting authority to consider, where 

appropriate, “the dilution of the effluent in the receiving water” when determining whether a 

discharge causes, has the reasonable potential to cause, or contributes to an instream excursion 

above a criterion. Depending on the state or tribal WQS and implementation policies, a 

consideration of dilution could be expressed in the form of a dilution allowance or a mixing zone. 

A dilution allowance typically is expressed as the flow or portion of the flow of a river or stream and 

is typically applied in flowing waters where rapid and complete mixing occurs. A mixing zone is 

typically applied in any waterbody type in which incomplete mixing occurs. For more information, 

see Chapter 6 of the NPDES Permit Writers’ Manual (2010). 

While mixing zones serve to dilute concentrations of pollutants in effluent discharges, they also allow 

increases in the mass loading of the pollutant to the waterbody (more so than would occur if no 

mixing zone were allowed). Therefore, if not applied appropriately, a mixing zone could adversely 

affect mobile species passing through the mixing zone as well as less mobile species (e.g., benthic 

communities) in the immediate vicinity of the discharge. Because of these and other factors, mixing 

zones should be applied carefully so that they do not result in impairment of the designated use of the 

waterbody as a whole or impede progress toward the CWA goals of restoring and maintaining the 

physical, chemical, and biological integrity of the Nation’s waters. Keeping this in mind, a state or 

tribe has the discretion to choose whether to authorize mixing zones and adopt a mixing zone 

policy. However, as described below, if a state or tribe chooses to adopt a mixing zone policy, such

a policy is generally considered a new or revised WQS that must be adopted into state or tribal law 

and approved by the EPA before it is effective for CWA purposes.

An important note is that “mixing zone” is used in multiple ways. A mixing zone policy is a legally 

binding state or tribal policy that is adopted into WQS and describes the general characteristics of and 

requirements associated with mixing zones without taking into account site-specific information. The 

EPA generally views such mixing zone polices as constituting new or revised WQS that require EPA 

review and approval or disapproval under Section 303(c) of the CWA. Consistent with the four-part 

test described in What is a New or Revised Water Quality Standard Under CWA Section 303(c)? 

Frequently Asked Questions (2012) and Chapter 1 of this Handbook, a state or tribal mixing zone 

policy is a legally binding provision that is adopted into state or tribal law (part one), and it 

addresses the criteria component of WQS (part two). Additionally, a mixing zone policy expresses a 

desired condition in the waterbody to allow flexibility in meeting the applicable criteria within 

certain areas of the waterbody (part three), and if it is a new provision or revises an existing policy 

(part four), it clearly meets the requirements to be a new or revised WQS.

On the other hand, an individual, site-specific mixing zone is authorized for a particular point-source 

discharge in accordance with a state or tribal mixing zone policy and accounts for the site-specific 

characteristics of a particular discharge and receiving water. An individual mixing zone is defined and 

implemented through the NPDES permitting process. The EPA does not view individual mixing zones 
3

as constituting new or revised WQS requiring EPA review under Section 303(c). Like a mixing zone 

policy, an individual mixing zone is a legally binding provision that is established pursuant to state 

or tribal law (part one), and it addresses the criteria component of WQS (part two). However, unlike 

a mixing zone policy, an individual mixing zone does not express or establish a desired condition 

in the waterbody (part three). Instead, the individual mixing zone is used to establish appropriate 

water quality-based effluent limits (WQBELs) for a specific discharger’s NPDES permit. An 

individual mixing zone also does not establish a new provision or revise an existing provision (part 

four). Rather, it implements a WQS (i.e., the state or tribal mixing zone policy) for a specific 

discharger using site-specific information.

Additionally, any time an effluent is discharged into a receiving water, there will be a zone of actual 

or physical mixing in which the discharge and receiving water naturally mix regardless of whether 

a mixing zone, in the regulatory sense, has been authorized. Such actual mixing is described using 

field studies and a water quality model and is used in establishing an individual, site-specific 

mixing zone for a particular discharge.

The authorization of mixing zones under incompletely mixed discharge and receiving water 

situations pre-dates the CWA. The EPA's current mixing zone guidance, contained in this 

Handbook, the Technical Support Document for Water Quality-based Toxics Control (TSD) (1991), 

and the NPDES Permit Writers’ Manual (2010), evolved from previous guidance from the EPA and its 

predecessor agencies on the use of mixing zones as a regulatory tool to address the incomplete 

mixing of wastewater discharges in receiving waters. This Handbook describes the EPA’s

recommendations for state and tribal mixing zone policies. The other two documents listed above 

describe the technical and permitting aspects of defining individual, site-specific mixing zones for 

point-source discharges during the NPDES permitting process. Additional information on mixing 

zones can also be found in the EPA’s Compilation of EPA Mixing Zone Documents (2006) and 

Advanced Notice of Proposed Rulemaking for Water Quality Standards (1998).

5.1.1 Recommended Contents of State and Tribal Mixing Zone Policies 

The EPA recommends that states and authorized tribes adopt, at a minimum, a definitive statement 

into their WQS specifying whether the state or tribe intends to authorize mixing zones. Consistent 

with the discussion above, where a mixing zone is authorized, water quality criteria are met at the 

edge of the mixing zone during critical low-flow conditions (which are described in Section 5.2 of 

this chapter) so that the designated use of the waterbody as a whole is protected. If a state or tribe 

chooses to adopt a mixing zone policy, such a policy should ensure the following:

 Mixing zones do not impair the designated use of the waterbody as a whole.

 Pollutant concentrations within the mixing zone are not lethal to organisms passing 

through the mixing zone.2

 

2 Lethality is a function of the magnitude of a pollutant concentration and the duration an 

organism is exposed to that concentration. Section 4.3.3 of the TSD (1991) describes various 
4

 Pollutant concentrations within the mixing zone do not cause significant human health 

risks considering likely pathways of exposure.

 Mixing zones do not endanger critical areas such as breeding or spawning grounds, 

habitat for threatened or endangered species, areas with sensitive biota, shellfish beds, 

fisheries, drinking water intakes and sources, or recreational areas.

Because pollutant concentrations may exceed numeric criteria within mixing zones, these elevated 

concentrations could adversely affect the productivity of the waterbody and have unanticipated 

ecological consequences. Therefore, the EPA recommends that the use of mixing zones in the 

development of WQBELs in NPDES permits be carefully evaluated and appropriately limited on a 

case-by-case basis in light of the overarching requirement to protect the designated use of the 

waterbody as a whole pursuant to 40 CFR 131.10.

Due to potential additive or synergistic effects of certain pollutants that could result in the 

designated use of the waterbody as a whole not being protected, state and tribal mixing zone 

policies should specify, and permitting authorities should ensure, that mixing zones do not 

overlap. Additionally, the EPA recommends that permitting authorities evaluate the cumulative 

effects of multiple mixing zones within the same waterbody. The EPA has developed a holistic 

approach to determine whether a mixing zone is appropriate based on such cumulative effects 

considering all of the impacts to the designated uses of the waterbody (see Allocated Impact Zones 

for Areas of Non-Compliance (1995)). If the total area affected by elevated concentrations within all 

mixing zones combined is small compared to the total area of the waterbody in which the mixing 

zones are located, then mixing zones are likely to have little effect on the designated use of the 

waterbody as a whole, provided that they do not impinge on unique or critical habitats. As 

understanding of pollutant impacts on ecological systems evolves, states and tribes may find 

specific cases in which no mixing zone is appropriate.

States and tribes that choose to adopt mixing zone policies should describe the general 

procedures for defining and implementing mixing zones in terms of location, maximum size, 

shape, outfall design, and in-zone water quality, at a minimum. Such policies should be sufficiently 

detailed to support regulatory actions, issuance of permits, and determination of best 

management practices for nonpoint sources. 

The EPA recommends that specific characteristics of an individual mixing zone for a specific 

discharger be defined on a case-by-case basis using the state or tribal mixing zone policy. This 

site-specific assessment would ideally take into consideration the physical, chemical, and 

biological characteristics of the discharge (including the type of pollutant discharged) and 

receiving waterbody; the life history and behavior of organisms in the receiving waterbody; and the 

designated uses of the waterbody. 

Location

 

methods for preventing lethality to organisms passing through a mixing zone.
5

States and authorized tribes should restrict the potential locations of mixing zones as a way to 

protect stationary benthic organisms and human health from the potential adverse effects of 

elevated pollutant levels. In addition, states and tribes should prohibit mixing zones where they

may endanger biologically important and other critical areas that the state, tribe, or federal 

government has identified. These include breeding and spawning grounds, habitat for threatened 

or endangered species, areas with sensitive biota, shellfish beds, fisheries, drinking water intakes 

and sources, and recreational areas. 

Pollutant concentrations above the chronic aquatic life water quality criterion may prevent sensitive 

taxa from living and reproducing successfully within the mixing zone. In this regard, benthic and 

territorial organisms may be of greatest concern in protecting aquatic life within a mixing zone. 

The higher the pollutant concentrations occurring within the mixing zone, the more taxa are likely 

to be adversely affected, thereby affecting the structure and function of the ecological community 

and, potentially, the designated use of the waterbody as a whole.

For protection of human health, states and tribes should restrict mixing zones such that they do

not result in significant human health risks when evaluated using reasonable assumptions about 

exposure pathways. For example, where drinking water contaminants are a concern, the mixing 

zones should not encroach on drinking water intakes and sources. Where fish tissue residues are a 

concern (either because of measured or predicted residues), mixing zones should not result in 

significant human health risks to average and sensitive subpopulations of consumers of fish and 

shellfish after considering exposure duration of the affected aquatic organisms in the mixing zone 

and the patterns of fisheries use in the area. Where waters are designated for primary contact 

recreation, mixing zones for bacteria should not result in significant human health risks to people 

recreating in such waters. In all cases, it is critical that the designated use of the waterbody as a 

whole is protected.

Size

In order to protect the designated uses of the waterbody as a whole, pollutant concentrations 

within any mixing zone should not be lethal to mobile, migrating, and drifting organisms in the 

waterbody or cause significant human health risks considering likely pathways of exposure. One 

means of achieving these objectives is to limit the size of the mixing zone. 

Most states and authorized tribes allow mixing zones as a matter of policy but also specify general 

spatial dimensions that limit their size. States and tribes have developed various methods of 

defining the maximum allowable size of mixing zones for various types of waters. State and tribal 

policies dealing with streams and rivers often limit mixing zone widths, cross-sectional areas, 

and/or flow volumes and allow lengths to be determined on a case-by-case basis. For lakes, 

estuaries, and coastal waters, dimensions are usually specified by surface area, width, 

cross-sectional area, and/or volume. The EPA recommends that states and tribes use methods that 

result in quantitative measures sufficient for permitting authorities to develop WQBELs in a 

transparent and straightforward manner.
6

If a mixing zone is authorized for a specific discharge, the permitting authority then defines the 

actual size of an individual, site-specific mixing zone for the specific discharge on a case-by-case 

basis using the general size restrictions in the state or tribal mixing zone policy. The area or 

volume of an individual mixing zone or group of mixing zones should be as small as practicable so 

that it does not interfere with the designated uses or with the established community of aquatic life 

in the segment for which the uses are designated. 

In general, where a state or tribe has both acute and chronic aquatic life water quality criteria as 

well as human health criteria for the same pollutant, states and tribes may establish independent 

mixing zone size specifications that apply to each criteria type. For aquatic life criteria, there may 

be up to two types of mixing zones: one for the acute criterion and one for the chronic criterion

(see Figure 5.1). 

In the zone immediately surrounding the outfall, both the acute and the chronic criteria may be 

exceeded, but the acute criterion is met at the edge of this zone, which is often referred to as the 

acute mixing zone or the zone of initial dilution. The acute mixing zone is sized to prevent lethality 

to passing organisms in order to protect the designated use of the waterbody as a whole. 

In the next mixing zone, which is often called the chronic mixing zone, the chronic criterion may 

be exceeded, but the acute criterion is met. The chronic criterion is met at the edge of the chronic 

mixing zone. The chronic mixing zone is sized to protect the designated use of the waterbody as a 

whole. 

Where the state or tribe also has human health criteria for the pollutant of concern, the human 

health mixing zone is sized to prevent significant human risks in order to protect the designated 

use of the waterbody as a whole. 
7

 

For a particular pollutant found in a particular discharge, the magnitude, duration, frequency, and

any authorized mixing zone associated with each of the criteria types (i.e., human health and acute 

and chronic aquatic life) will determine which criterion most limits the allowable discharge. In all 

cases, the permitting authority should evaluate the size of the site-specific mixing zone to determine

its effect on the designated use of the waterbody as a whole. Section 2.2.2 of the TSD (1991) contains 

information for determining whether a mixing zone’s size is appropriate. 

State and tribal mixing zone policies should identify zones of passage within waterbodies that 

contain migrating, free-swimming, or drifting organisms. Zones of passage are continuous water 

routes of such volume, area, and quality as to allow the passage of free-swimming and drifting 

organisms without significant adverse effects on their populations. Many species migrate for 

spawning and other purposes. Not only do migrating species (e.g., anadromous and catadromous 

species) need to be able to reach suitable spawning areas, their young (and in some cases the 

adults) require a safe return route to their growing and living areas. Elevated pollutant 

concentrations within a mixing zone can create barriers that hinder or prevent safe migration. 

Therefore, mixing zones should be sized and located appropriately within the waterbody to 

provide a continuous zone of passage that protects migrating, free-swimming, and drifting 

organisms. 

Shape

The waterbody type, outfall design, and characteristics of the discharge will determine the shape of 

a mixing zone. The shape should be a simple configuration that is easy to locate in a waterbody 

and that avoids impingement on biologically important areas. In lakes, a circle with a specified 

radius is generally preferable, but other shapes may be appropriate in the case of unusual site 

Outfall

Acute Criterion Met

Chronic Criterion Met

Acute Mixing Zone

Chronic Mixing Zone

Figure 5.1: Example Mixing Zones for Acute and Chronic Aquatic Life Criteria
8

requirements. 

"Shore-hugging" plumes should be avoided in all waterbodies. Shore areas are often the most 

biologically productive and sensitive areas of a waterbody, and they are often used for recreation.

Shore-hugging plumes generally do not mix as well with receiving waters and, thus, do not dilute 

as well as mixing zones with other shapes that do not hug shorelines. Because shore-hugging 

plumes tend to keep unmixed water over the benthic area or in the recreational area, they are more 

likely to adversely affect the designated uses of the waterbody.

Outfall Design

Because outfall design affects the amount of initial mixing that occurs, state and tribal mixing zone 

policies should instruct dischargers to utilize the best practicable engineering design of the outfall

to maximize initial mixing. Sometimes, modifying the design of the diffuser, the location of the 

outfall, or other outfall design characteristics can reduce significant adverse impacts to the 

waterbody because different design characteristics have different effects on mixing. Many 

different factors affect how well the outfall design allows the discharge to mix with the receiving 

water including the following:

 The height of the outfall with respect to the surface and bottom of the waterbody.

 The distance of the end of the pipe to the nearest bank (i.e., whether the outfall is in the 

middle of the waterbody or close to one side).

 The angle of the discharge.

 The type of diffuser that is used (i.e., single-port or multi-port diffuser). 

Section 4.4.1 of the TSD (1991) describes recommendations for outfall design in more detail. 

In-zone Water Quality

States and authorized tribes should ensure that a minimum level of water quality is maintained

within a mixing zone. Mixing zones should attain the “free from” narrative water quality criteria 

that are applicable to all waters in a state or reservation. For example, the EPA recommends that 

mixing zones be free from the following:

 Materials in concentrations that will cause acutely toxic conditions to aquatic life.

3

 Materials in concentrations that settle to form objectionable deposits.

 Floating debris, oil, scum, and other material in concentrations that form nuisances.

 Substances in concentrations that produce objectionable color, odor, taste, or turbidity.

 

3 Acutely toxic conditions are those that are lethal to aquatic organisms that may pass through the 

mixing zone. The underlying assumption for allowing a mixing zone is that pollutant 

concentrations in excess of acute and chronic criteria, but below acutely toxic concentrations, may 

exist in small areas without causing adverse effects to the designated use of the waterbody as a 

whole.
9

 Substances in concentrations that produce undesirable aquatic life or result in a dominance of 

nuisance species.

5.1.2 Situations in Which Mixing Zones May Not Be Appropriate 

As discussed above, states and authorized tribes are not required to allow mixing zones. Even if a 

state or tribe chooses to allow mixing zones generally, it may also choose to define in its policy 

circumstances under which mixing zones are prohibited (e.g., for particular pollutants and/or 

waterbodies). Likewise, where the state or tribe generally allows mixing zones, the permitting 

authority may decide that a mixing zone is not appropriate for a particular discharge on a 

site-specific basis.

4 States and tribes should conclude that mixing zones are not appropriate in 

the following situations:

 Where they may impair the designated use of the waterbody as a whole.

 Where they contain pollutant concentrations that may be lethal to passing organisms.

 Where they contain pollutant concentrations that may cause significant human health risks 

considering likely pathways of exposure.

 Where they may endanger critical areas such as breeding and spawning grounds, habitat 

for threatened or endangered species, areas with sensitive biota, shellfish beds, fisheries, 

drinking water intakes and sources, and recreational areas.

Additionally, states and tribes should carefully consider whether mixing zones are appropriate 

where a discharge contains bioaccumulative, pathogenic, persistent, carcinogenic, mutagenic, or 

teratogenic pollutants or where a discharge containing toxic pollutants may attract aquatic life. 

Bioaccumlative pollutants are one example of a pollutant for which mixing zones may not be 

appropriate because they may cause significant human health risks such that the designated use of 

the waterbody as a whole may not be protected.

5 Therefore, the EPA recommends that state and 

tribal mixing zone policies do not allow mixing zones for discharges of bioaccumulative 

pollutants. The EPA adopted this approach in 2000 when it amended its 1995 Final Water Quality 

Guidance for the Great Lakes System at 40 CFR Part 132 to phase out mixing zones for existing 

discharges of bioaccumulative pollutants within the Great Lakes Basin and ban such mixing zones 

for new discharges within the Basin.

Because fish tissue contamination tends to be a far-field problem affecting entire or downstream

waterbodies rather than a near-field problem being confined to the area within a mixing zone, a 

state or tribe may find it appropriate to restrict or eliminate mixing zones for bioaccumulative 

 

4 The 1996 memorandum EPA Guidance on Application of State Mixing Zone Policies in EPA-issued 

NPDES Permits describes the circumstances under which the EPA may include a mixing zone in an 

NPDES permit when the EPA is the permitting authority.

5

However, note that some chemicals of relatively low toxicity such as zinc will bioconcentrate in 

fish without harmful effects resulting from human consumption.
10

pollutants in certain situations such as the following: 

 Where mixing zones may encroach on areas often used for fish harvesting, particularly for

stationary species such as shellfish. 

 Where there are uncertainties in the protectiveness of the water quality criteria or the 

assimilative capacity of the waterbody.

Chapter 3 of this Handbook and Chapter 5 of Methodology for Deriving Ambient Water Quality 

Criteria for the Protection of Human Health (2000) provide additional information about

bioaccumulation, and Section 4.3.4 of the TSD (1991) discusses preventing bioaccumulation 

problems for human health in calculating WQBELs.

Another example of a pollutant for which a mixing zone may not be appropriate is bacteria. 

Because bacteria mixing zones may cause significant human health risks and endanger critical 

areas (e.g., recreational areas), the EPA recommends that state and tribal mixing zone policies do 

not allow mixing zones for bacteria in waters designated for primary contact recreation. The 

presumption in a river or stream segment designated for primary contact recreation is that primary 

contact recreation can safely occur throughout the segment and, therefore, that bacteria levels will 

not exceed criteria throughout the segment. Epidemiological studies have demonstrated that

illness rates are higher when the criteria are exceeded compared to when those criteria are not 

exceeded (see Sections 3.2 and 3.3 of the EPA's Recreational Water Quality Criteria (2012)). 

Therefore, people recreating in or through a bacteria mixing zone (where bacteria levels may be 

elevated above the criteria levels) may be exposed to greater risk of gastrointestinal illness than 

would otherwise be allowed by the state or tribal criteria for protection of the recreation use. Given 

this presumption, states and tribes should carefully evaluate whether authorizing a mixing zone 

that results in elevated levels of bacteria in a river or stream designated for primary contact 

recreation will adversely affect the designated use. If so, then states and tribes should not 

authorize such mixing zones because they could result in a significant human health risk.

A third example of a situation in which the EPA recommends that states and tribes prohibit a mixing 

zone is when an effluent is known to attract biota. In such cases, a continuous zone of passage 

around the mixing area will not protect aquatic life. Although most toxic pollutants elicit a neutral or 

avoidance response, there are some situations in which aquatic life are attracted to a toxic discharge 

and, therefore, can potentially incur significant exposure. For example, temperature can be an 

attractive force and may counter an avoidance response to a particular pollutant. Therefore, the 

organisms would tend to stay in the mixing zone rather than passing through or around it. Innate 

behavior such as migration may also counter an avoidance response and cause fish to incur 

significant exposure.

5.1.3 Mixing Zones for the Discharge of Dredged or Fill Material 

In conjunction with the Department of the Army, the EPA has developed guidelines at 40 CFR Part

230 for evaluating discharges of dredged or fill material into navigable waters, which include
11

provisions at 40 CFR 230.11(f) for determining the acceptability of mixing zones for such material. 

Discharges of dredged or fill material are generally temporary and result in short-term disruption 

to the waterbody rather than constituting a continuous discharge with long-term disruption

beyond the fill area. In authorizing and establishing mixing zones for dredge and fill activities, the 

state or authorized tribe’s primary consideration should be achieving and protecting the 

designated uses of the waterbody pursuant to 40 CFR 131.10. As such, states and tribes should 

evaluate the particular pollutants involved for their effects on the designated use. Technical 

guidance for determining the potential for contaminant-related impacts associated with the 

discharge of dredged material can be found in Evaluation of Dredged Material Proposed for 

Discharge in Waters of the U.S. – Testing Manual: Inland Testing Manual (1998).

5.1.4 Mixing Zones for Aquaculture Projects 

Under Section 318 of the CWA, permitting authorities may allow discharges of certain pollutants

associated with approved aquaculture projects. Consistent with 40 CFR 122.25, an aquaculture 

project is a defined, managed water area into which certain pollutants are discharged for the 

maintenance or production of harvestable freshwater, estuarine, or marine plants or animals. The

EPA’s regulations at 40 CFR 125.11 provide that aquaculture project approval must not result in 

the enlargement of a pre-existing mixing zone beyond the area designated for the original 

discharge and that the designated project area (which is also defined at 40 CFR 122.25) must not 

include a portion of a waterbody large enough to expose a substantial portion of the indigenous 

biota to the conditions within the designated project area. For example, a designated project area 

should not include the entire width of a stream because all of the indigenous organisms might be 

exposed to pollutant discharges that would exceed WQS. The areas designated for approved 

aquaculture projects should be treated in the same manner as other mixing zones.

5.2 Critical Low Flows for Water Quality Criteria Implementation 

Pursuant to 40 CFR 131.11(a), states and authorized tribes must adopt those water quality criteria 

that protect designated uses. To ensure that adopted criteria are protective of the designated uses, 

states and tribes generally establish critical low-flow values to support implementation of the 

applicable criteria through such programs as NPDES permitting. 

Critical low-flow conditions present special challenges to the integrity of the aquatic community 

and the protection of human health. Dilution is one of the primary mechanisms by which the 

concentrations of contaminants in effluent discharges are reduced following their introduction into 

a receiving water. Low flows in the receiving water typically aggravate the effects of effluent 

discharges because, during a low-flow event, there is less water available for dilution, resulting in 

higher instream concentrations of pollutants. Therefore, the allowable dilution (which may be only 

a portion of the critical low flow depending on the state or tribal WQS and implementation 
12

procedures) for purposes of determining the need for and establishing WQBELs in NPDES permits 

should ensure protection of the applicable criteria at the calculated critical low-flow value. 

The EPA has historically encouraged states and tribes to specify directly within their WQS which 

calculated critical low-flow values should be used to determine the available dilution for the 

purposes of determining the need for and establishing WQBELs. Such critical low-flow values have 

historically been reviewed and approved or disapproved by the EPA as new or revised WQS under 

Section 303(c) of the CWA. Likewise, revisions to those critical low-flow values would generally 

constitute new or revised WQS subject to EPA review and approval or disapproval (see Chapter 1 of 

this Handbook and What is a New or Revised Water Quality Standard Under CWA Section 303(c)? 

Frequently Asked Questions (2012)). 

Most states and tribes generally follow the guidance in the TSD (1991) when adopting critical 

low-flow values for criteria implementation. The EPA recommends that states and tribes adopt the 

critical low-flow values for use in steady-state analyses so that criteria are implemented 

appropriately. If criteria are implemented using inappropriate critical low-flow values (i.e., 

calculated values that are too high), the resulting control of toxic pollutants may not be fully 

protective because the resulting ambient concentrations could exceed criteria when such low flows 

occur. In the case of aquatic life, more frequent excursions than are allowable (e.g., more than 

once in three years) could result in unacceptable effects on aquatic organisms and designated uses

if the appropriate value is not used in the calculations.

In addition to steady-state models, the TSD recommends the use of three dynamic models to 

perform wasteload allocations. Because dynamic wasteload models do not generally use specific 

steady-state critical low-flow values but accomplish the same effect by factoring in the probability 

of occurrence of stream flows based on the historical flow record, this Handbook discusses only 

steady-state conditions. 

In Appendix D of the TSD and Technical Guidance Manual for Performing Wasteload Allocations, 

Book VI: Design Conditions – Chapter 1: Stream Design Flow for Steady-State Modeling (1986), the 

EPA describes and recommends two methods for calculating acceptable critical low-flow values: 

the traditional hydrologically based method developed by the United States Geological Survey

(USGS) and a biologically based method developed by the EPA.6 The hydrologically based critical 

low-flow value is determined statistically using probability and extreme values, while the 

biologically based critical low flow is determined empirically using the specific duration and 

frequency associated with the criterion.

Additionally, the two documents listed above describe the flow values that the EPA recommends 

for implementing acute and chronic criteria using both methods. Table 5.1 below summarizes 

these recommendations.

 

6 In some EPA documents such as those cited, critical low flow is also called “design flow” or 

“stream design flow.” These terms are different from a facility or effluent design flow.
13

Table 5.1: EPA-recommended Critical Low Flows for Aquatic Life and Human Health Criteria 

Criteria Hydrologically Based Flow Biologically Based Flow 

Acute Aquatic Life 1Q10 1B3

Chronic Aquatic Life 7Q10 4B3

Human Health Harmonic mean

Using the hydrologically based method, 1Q10 represents the lowest one-day average flow event 

expected to occur once every ten years, on average, and 7Q10 represents the lowest 

seven-consecutive-day average flow event expected to occur once every ten years, on average. 

Using the biologically based method, 1B3 represents the lowest one-day average flow event 

expected to occur once every three years, on average, and 4B3 represents the lowest 

four-consecutive-day average flow event expected to occur once every three years, on average. 

States and tribes may designate other critical low-flow values to implement the applicable criteria, 

provided they are scientifically justified. The EPA has also recommended critical low-flow values 

that differ from the above recommendations for specific pollutants such 30Q5, 30Q10, and 30B3 

for implementing chronic criteria for ammonia. 

The EPA does not view the fact that many streams within a state or tribe have no flow at 7Q10 as 

adequate justification for designating alternative flows. Note that, when a criterion specifies a 

four-day average concentration that should not be exceeded more than once every three years, 

this condition should not be interpreted as implying that a 4Q3 low flow is appropriate for use as 

the hydrologically based critical low-flow value for assessing impacts on the receiving water. 

The EPA recommends the harmonic mean flow for implementing human health criteria. The 

concept of a harmonic mean is a standard statistical data analysis technique. The EPA's model for 

human health effects assumes that such effects occur because of a long-term exposure to low 

concentrations of a toxic pollutant (e.g., two liters of water per day for seventy years). The 

harmonic mean flow allows for estimating the concentration of toxic pollutant contained in those 

two liters of water per day when the daily variation in the flow rate is high. Therefore, the EPA 

recommends use of the harmonic mean flow in computing critical low flows for human health 

criteria rather than using other averaging techniques. 

In addition to the documents listed above, see the EPA’s Flow 101 webpage and Advanced Notice of 

Proposed Rulemaking for Water Quality Standards (1998) for additional information on critical low 

flows. 

The EPA notes that the USGS has documented that, in some areas of the United States, there have 

been changes to the critical low flows in freshwater rivers and streams or increased duration and 

frequency of low flow occurrence. The source of the reductions may often be anthropogenic in 

origin such as over-pumping of groundwater, hydrologic alteration including impoundments, or 

surface water withdrawals. Some of these reductions may persist long enough to cause changes to 

the critical low-flow values. In addition, prolonged droughts have resulted in a reduction of the 

low-flow minimums released on regulated rivers or revisions to drought control manuals to allow 
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for further reductions of the low-flow values. During prolonged droughts, there may also be a 

trend towards increased pumping of groundwater, which may, in turn, lead to a reduction of 

surface water flows. New water intakes may also permanently change a waterbody’s critical low 

flow. The following documents provide additional information on changing flow patterns:

 The USGS’s National Water Census - Streamflow webpage.

 The USGS’s Groundwater Depletion in the United States (1900-2008) (2013).

 The USGS’s Alteration of Streamflow Magnitudes and Potential Ecological Consequences: a 

Multiregional Assessment (2011).

 The EPA’s Report on the Environment – Fresh Surface Water webpage.

It may be prudent for states and tribes to review and revise, as appropriate, their critical low-flow

values during the triennial review process to account for changes to historical flow patterns. Also, 

NPDES permitting authorities should be aware that these altered historical flow patterns in rivers 

and streams may render historical flow records less accurate in predicting current and future 

critical flows. Where appropriate, permitting authorities should consider alternate approaches to 

establishing critical low-flow conditions that account for these climatic and anthropogenic 

changes when conducting reasonable potential analyses and in establishing protective WQBELs

(see NPDES Permit Writers’ Manual: Inclusion of Climate Change Considerations).

 
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5.3 Variances from Water Quality Standards 

A WQS variance is a time-limited designated use and water quality criterion for a specific 

pollutant(s) or water quality parameter(s) that reflect the highest attainable condition during the 

term of the WQS variance. A WQS variance may apply to an NPDES-permitted discharger or 

waterbody/waterbody segment(s). The regulation at 40 CFR 131.13 provides that states and 

authorized tribes may adopt into their WQS general variance policies that describe how they intend 

to apply and implement variances. Although such variance policies require EPA review and 

approval, states and tribes are not required to adopt variance policies in order to adopt individual 

variances. Nevertheless, as opposed to individual mixing zones (discussed in Section 5.1 of this 

chapter), the individual variances themselves must be adopted into WQS (or other legally binding 

state or tribal requirements) and approved by the EPA before they can be effective for CWA

purposes.

Although the legal authority to adopt a WQS variance is the same as a revision to a designated use, 

the purpose of a variance is different from that of a designated use revision (described in Chapter 

2 of this Handbook). A variance is intended to serve as a mechanism to provide time for states, 

tribes, and stakeholders to implement actions to improve water quality over an identified period of 

time when and where the designated use currently in place is not being met. When utilizing a 

variance, the state or tribe retains the designated use that is currently in place as a long-term goal. 

As first articulated in 1977 in Decision of the General Counsel on Matters of Law Pursuant to 40 

CFR Section 125.36(m). No. 58, a state or tribe may adopt a WQS variance if the state or tribe can 

satisfy the same substantive and procedural requirements as a designated use removal, which are 

described in 40 CFR 131.10(g). 

A variance is also different from a permit compliance schedule. While both tools can provide time 

to meet regulatory requirements, which tool is appropriate depends upon the circumstances. 

Variances can be appropriate to address situations where it is known that the designated use and 

criterion are unattainable today (or for a limited period of time), but feasible progress could be 

made toward attaining the designated use and criterion. A permit compliance schedule, on the 

other hand, may be appropriate when the designated use is attainable, but the discharger needs 

additional time to modify or upgrade treatment facilities in order to meet its WQBEL such that a 

schedule and resulting milestones will lead to compliance “as soon as possible” with the WQBEL 

based on the currently applicable WQS. See CWA Section 502(17) for a definition of “schedules of 

compliance” and 40 CFR 122.47. 

A variance may be appropriate where a state or tribe determines that the designated use cannot be 

attained for a period of time because the discharger cannot immediately meet a WQBEL, which is 

written to meet a particular WQS, or a waterbody/waterbody segment cannot immediately meet the 

criteria to protect the designated use. Under such circumstances, the variance provides a targeted, 

time-limited revision to the WQS that reflects the highest attainable condition. These new 

time-limited WQS then serve as the basis for pollution control requirements during the term of the 
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variance. For WQS variances that apply to aquatic life, wildlife, and recreational uses (i.e., the

Section 101(a)(2) uses), this means that attainment of the designated use is infeasible under at 

least one of the six factors at 131.10(g) for at least the term of the variance. 

The practical effect of the variance is an NPDES permit containing a WQBEL that complies with a less 

stringent criterion than would otherwise be in effect in the absence of the variance. However, the 

underlying designated use and criteria remain in effect for Section 303(d) listing and total 

maximum daily load development regardless of whether the variance is for a single discharger, 

multiple dischargers, or a waterbody/waterbody segment. At the end of the variance term, the 

discharger’s WQBEL must ensure compliance with the underlying designated use and criterion or 

the state or tribe must obtain a new variance. To obtain a new variance, the state or tribe must 

again demonstrate that the designated use is not attainable at the point of discharge and again 

submit the variance to the EPA for review and approval or disapproval.

In many cases, a WQS variance is an environmentally useful tool because a variance exists only for 

a defined term and retains designated use protection for all pollutants and sources, with the sole 

exception of those specified in the variance. Even the discharger with a variance for a particular 

pollutant is required to meet applicable criteria for all other pollutants. Thus, a variance can result 

in water quality improvements over time and, in some cases, full attainment of designated uses by 

maintaining existing water quality protections while allowing time for advances in treatment 

technologies, control practices, or other changes in circumstances.

States and tribes typically adopt a WQS variance for an individual discharger for a specific pollutant 

in a specific waterbody. However, where multiple dischargers have similar attainment challenges, a 

state or tribe may streamline its variance process by adopting a multiple-discharger WQS variance. 

Such a variance applies to several dischargers but may be supported by a single technical rationale 

justifying the need for the variance. The EPA has previously published information on both 

individual- and multiple-discharger variances at 40 CFR Part 132. For additional information on 

variances, also see Discharger-Specific Variances on a Broader Scale: Developing Credible 

Rationales for Variances that Apply to Multiple Dischargers (2013).