CHAPTER 3 

Issue Category: Variances 

Pages 3-290 – 3-408

Response to Public Comments

Water Quality Standard Regulatory Revisions

August, 2015

40 CFR Part 131

Docket #: EPA-HQ-OQ-2010-0606

This document is part of a larger document.
Chapter 3 – Response Essays 8.a – Var – Gen Supp 

Essay 8.a – Variances: General Support

A. General Support

The U.S. Environmental Protection Agency (EPA) thanks the commenters for supporting the concept of 

providing for water quality standards (WQS) variances in the regulation and for the time, effort and 

thought commenters invested in providing the EPA with meaningful input.

B. Requirements Result in Additional Administrative Burden

EPA revised the proposed rule to minimize administrative burden while also fulfilling EPA’s regulatory 

objectives. EPA estimates of the potential incremental burden and cost associated with the final rule are 

summarized in the rule preamble. The complete economic analysis (EA) to the final rule can be obtained 

from docket No. EPA–HQ–OW–2010–0606. Further discussion of comments on the EA can be found in 

Essay 12.b.

C. Water Quality Standards Variance Adoption and Streamlining and Multiple 

Discharger Variances

Each WQS variance is, itself, a change to WQS because it represents a change to the desired condition of 

a water body (albeit limited in time and scope) and/ or mandates how it will be expressed in the future. 

Clean Water Act (CWA) section 303(c) and EPA’s implementing regulation at section 131.5 specify that 

EPA must review and approve or disapprove any new or revised WQS. States and authorized tribes must 

adopt any WQS variance into their WQS because the National Pollutant Discharge Elimination System 

(NPDES) permit regulation at section 122.44(d)(vii)(A) requires the permitting authority to develop 

water quality-based effluent limits (WQBELs) that derive from and comply with all applicable WQS. If a 

state or authorized tribe does not adopt a WQS variance as a legally binding WQS, the permitting 

authority would be unable to reflect the less stringent interim WQS of the WQS variance in the NPDES 

permit. See also EPA’s response to code 8.f.i – Variances Applicability: Scope for a full discussion on why 

WQS variances are WQS.

Although states and authorized tribes must adopt a WQS variance into state WQS, there are ways for a 

state or authorized tribe to streamline the WQS variance process and reduce the administrative burden 

associated with adopting WQS variances as legally binding WQS. As explained in the preamble to today’s 

rule, a state or authorized tribe could adopt a single WQS variance for more than one discharger if all 

the dischargers are experiencing challenges meeting their WQBELs for the same pollutant for the same 

reason, even if they are not discharging to the same water body. In this situation, the state or authorized 

tribe may grant one variance that applies to all these dischargers (i.e., a multiple discharger variance) so 

long as the variance is consistent with the CWA and implementing regulations. The EPA recognized the 

utility of multiple discharger variances and their distinction from individual discharger variances in the 

‘‘Water Quality Guidance for the Great Lakes System: Supplementary Information Document’’ (SID; 

EPA–820– B–95–001; March 1995). The EPA provided further clarification regarding multiple discharger 

variances in the ‘‘Water Quality Standards for the State of Florida’s Lakes and Flowing Waters; Final 

Rule’’ (75 FR 75790, December 6, 2010). More recently in March 2013, the EPA provided a set of 

frequently asked questions (FAQ) to assist states and tribes in developing appropriate justifications for

multiple discharger variances (see: Discharger-specific Variances on a Broader Scale: Developing 

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Credible Rationales for Variances that Apply to Multiple Dischargers, EPA–820–F–13–012, March 2013 

(http://water.epa.gov/scitech/swguidance/standards/upload/Discharger-specific-Variances-on-aBroader-Scale-Developing-Credible-Rationales-for-Variances-that-Apply-to-Multiple-DischargersFrequently-Asked-Questions.pdf). See also section II.E (“What is EPA’s Position on Certain Public

Comments?”) of the preamble to the final rule for a discussion on other approaches to streamlining the

WQS variance process.

For further discussion on EPA’s oversight role, streamlining, multiple discharger variances and water

body variances see Essay 8.f.i. For further discussion regarding variance term (time frame) and 

expiration dates see Essay 8.g.iii. 

D. Other, Non-Variance-Specific Comments

As one commenter noted, EPA's current proposal does not include clarifications regarding either 

temporary modifications or ambient-based criteria. EPA notes that the use of either temporary 

modifications or ambient-based criteria must be consistent with the CWA and Title 40 of the Code of 

Federal Regulations (CFR) Part 131. 

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Essay 8.b – Variances: General Opposition

A. Variance Regulations Are Not Necessary

In 1977, an Office of General Counsel decision set forth the U.S. Environmental Protection Agency’s 

(EPA’s) legal position that it would be appropriate under the then existing regulations for a state to 

temporarily downgrade a water quality standard (WQS) as it applies to a specific discharger rather than 

permanently downgrading the WQS for the entire water body or waterbody segment(s), so long as such

variances met the substantive and procedural requirements for permanently downgrading a designated 

use. Prior to today’s final rule, there were no regulations specifically authorizing a state to adopt a 

variance that changed the applicable WQS. The Office of General Counsel decision concluded that while 

the then existing regulations did not specifically authorize a time-limited revision to WQS for a single 

discharger, if the state satisfied the requirements for revising the WQS (downgrading the use), the state 

could chose to adopt a more protective revision to its WQS due to its limited time and scope. This 

practice became known as adopting a WQS variance. In its 1983 WQS rulemaking, EPA referred to 

variances in Title 40 of the Code of Federal Regulations (CFR) section 131.13, a provision that provides 

states with authority to adopt various policies as part of their WQS. This provision indicates that 

variance policies are general policies affecting the application and implementation of WQS, and that 

states and tribes may include variances policies in their state and tribal standards, at their discretion. 

Even if a state or authorized tribe decided to adopt a policy for issuing variance, the adoption of 

individual variances are new or revised WQS and as such, section 303(c) of the Clean Water Act (CWA) 

requires EPA to review and approve or disapprove on the basis of whether they are consistent with

the Act.

EPA disagrees with commenters stating that there is no reason to establish regulations for WQS 

variances. EPA has heard from states, tribes, and stakeholders that there is confusion, inconsistency, 

and mixed interpretations about how, when, and where WQS variances may be used appropriately.

Where WQS variances could have led to significant water quality progress, a lack of a regulatory 

framework has, instead, resulted in little or no progress. Where states and authorized tribes (and their 

stakeholders) have more specificity in regulation regarding WQS variances such as those states and 

tribes covered by the “Water Quality Guidance for the Great Lakes System” rulemaking at 40 CFR part 

132, EPA has found that they have more success adopting and submitting WQS variances compared to 

states and tribes without such specificity.

WQS variances are an underutilized tool nationally. Since starting to track WQS variance submittals in 

2004, EPA has found that states/tribes in four regions have never submitted a variance as a WQS and 

states/tribes in 3 additional regions have not submitted a WQS variance since 2009. However, EPA has 

found that states and tribes covered by the Great Lakes Initiative (GLI) are successfully adopting and 

submitting WQS variances. Since 2004, 93 of the 135 WQS variances submitted to EPA were from states 

in Region 5 (which is covered by the GLI). See also sections I.C and II.E of the preamble to the final rule 

for additional discussion on the environmental issues the final rule addresses and for EPA’s rationale for 

including WQS variance provisions in the final regulations.

An example of an area of confusion under the prior regulations is whether WQS variances must adhere 

to all the same regulatory provisions as designated use changes, including whether or not a state must 

use the “attainability factors” to support a WQS variance for uses not specified in CWA section 101(a)(2) 

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(e.g., public water supply use, agricultural use, irrigation use). Comments that asserted there was no 

need for a specific WQS variance regulation in effect reflected the need for a regulation specifically for

WQS variances. The comments often disputed that there were existing federal requirements applicable 

to the adoption of WQS variances or that WQS variances required EPA approval. Those positions are 

evidence of the confusion surrounding the existing requirements regarding the adoption of WQS 

variances. They are also contrary to EPA’s interpretation of its regulations for over the past 30 years. The 

final rule will remove confusion regarding the status of WQS variances as acceptable revisions to WQS 

and the requirements for adopting WQS variances and submission to EPA for review and approval.

After decades of experience with WQS variances without specific regulation, EPA believes that codifying 

expectations for WQS variances will provide greater transparency, regulatory certainty, and national 

consistency to the WQS variance process. The final rule will significantly reduce confusion and mixed 

interpretations about how, when, and where WQS variances may be used. The regulation will also 

provide a strong signal to states, tribes, and the public that the legitimate use of WQS variances can 

ultimately improve water quality. By providing specific regulatory provisions that articulate both the 

flexibilities and accountability expectations of WQS variances, states, tribes and the public will have a 

consistent and transparent means to discuss strategies to incrementally improve water quality, which 

will remove barriers to the appropriate use of WQS variances and allow states and tribes to better 

address water quality challenges. The preamble to the final rule contains additional information about 

the need to establish WQS variance regulations.

B. Limits States’ Ability and Flexibilities to Use Water Quality Standards

Variances

WQS variances are intended to be used by states and authorized tribes when applicable designated uses

are not attainable in the near-term but may be attainable in the future. States and authorized tribes 

may use one or more WQS variances to require incremental improvements in water quality leading to 

eventual attainment of the ultimate designated use. If a state or authorized tribe believes the current 

designated use in not appropriate, the state or authorized tribe should not seek a WQS variance, but 

instead perform the required analysis (i.e., a use attainability analysis (UAA) for CWA 101(a)(2) uses or a 

“use and value” demonstration for non-101(a)(2) uses) to determine the appropriate designated use for 

the water body. In such a case, a WQS variance is not an appropriate WQS tool because time is not the 

issue with respect to attainability; rather a WQS variance is only appropriate when the state or 

authorized tribe believes the current designated use may be attainable, but needs time to implement 

adaptive management activities or wait for conditions to change such that the designated use becomes 

attainable.

Commenters suggest this final rule will limit rather than promote the use of WQS variances because 

some states already have WQS variance policies, and the new regulations may limit or prohibit some 

practices articulated in those policies. Some commenters identified practices that are not consistent 

with existing requirements regarding adoption of WQS variances and the need for EPA review and 

approval. To the extent current state policies are inconsistent with the current requirements regarding 

adoption of WQS variances (as new and revised WQS), which demonstrates the need for specific 

regulations articulating the requirements for the adoption of WQS variances. Where states and 

authorized tribes have binding WQS variance policies and/or procedures inconsistent with today’s rule, 

those states and authorized tribes will need to revise such policies and/or procedures as necessary to be 

consistent with the federal regulations if the state or authorized tribe wants to continue to adopt WQS

variances. This should occur prior to, or simultaneously with, adopting the first WQS variance, consistent 

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with the timeframe described in the effective date discussion in section I.E of the final preamble. States, 

authorized tribes, and stakeholders will benefit from this final rule even if state or tribal variance policies 

differ from the WQS variance regulations at section 131.14 because the requirements for EPA approval 

of a WQS variance are now clearly articulated. A clear initial understanding of EPA expectations for WQS 

variances has the potential to save states, authorized tribes, and stakeholders time and resources when 

preparing WQS variances and supporting documentation. Potential revisions to state or authorized tribal 

variance policies resulting from this final rule should not result in undue burden because such a revision 

would only need to occur once. EPA estimates the burden and cost of revising variance policies in its 

economic analysis (EA) of this final rule which can be found in docket number EPA–HQ–OW–2010–0606. 

Commenters expressed concerns about a lack of flexibility in the proposed WQS variance regulations. In 

response to these comments, EPA made several substantive revisions to the rule to provide additional 

flexibility to states and authorized tribes. Chief among them was to eliminate the 10-year maximum 

WQS variance term. The final rule does not specify a maximum WQS variance term, and instead allows 

the state or authorized tribe to specify the WQS variance term provided it is adequately justified in the 

supporting documentation that must be submitted to EPA with the WQS variance for review and 

approval or disapproval. In addition, the final rule allows states and authorized tribes to express the 

highest attainable condition (HAC) in three different ways, provides additional clarity on the type of 

demonstration needed for a WQS variance for a use or sub-category of a use not specified in CWA 

section 101(a)(2), allows states and authorized tribes to adopt subsequent WQS variances if justified, 

and adds additional water body types that may qualify for a WQS variance to implement restoration 

activities.

One comment asserted that EPA’s regulation would “effectively federalize” state policies. EPA is not 

federalizing state policies. EPA is setting minimum federal requirements for WQS variances to establish a 

level playing field for all states. States continue to have full discretion whether to adopt WQS variances.

There is no federal requirement to adopt WQS variances.

With regard to the comment requesting what constitutes a “structured scientific analysis,” EPA directs 

the commenter to EPA’s previous guidance in the “Water Quality Standards Handbook” 

(http://water.epa.gov/scitech/swguidance/standards/handbook/index.cfm) as well as UAA case studies 

on EPA website at http://water.epa.gov/scitech/swguidance/standards/uses/uaa/. EPA notes that, as 

described by the commenter, National Pollutant Discharge Elimination System (NPDES) Permit DMR can 

be useful in informing a UAA; however, it is unlikely that discharge monitoring report data alone will be 

sufficient to support a demonstration based on one of the six factors in section 131.10(g) or the new 

restoration factor in section 131.14. See also EPA’s response essay for 8.g.vi.

C. Water Quality Standards Variances Do Not Result in Water Quality 

Improvements/ Send Mixed Messages

EPA disagrees with commenters’ assertions that WQS variances will not lead to water quality 

improvements and attainment of designated uses and/ or send mixed messages. The final rule includes 

several provisions to ensure that states and authorized tribes use WQS variances appropriately to make 

progress toward achieving designated uses. The same incentive for incremental progress does not exist 

in the context of a designated use removal. Furthermore, EPA disagrees with commenters asserting that 

the final rule will not result in pollutant reductions by the discharger(s) to whom a WQS variance is 

applicable. Because the this final rule requires the state or authorized tribe to specify the HAC as the 

interim WQS, and the permitting authority must develop enforceable permit requirements consistent 

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with the interim WQS of the WQS variance (the NPDES regulation requires all NPDES permits to derive 

from and comply with all applicable WQS (section 122.44(d)), the NPDES permit will include enforceable 

permit requirements that will lead to the highest water quality attainable as identified in the WQS 

variance process. In such cases, the state and authorized tribe may work with their permittees to 

identify the highest attainable effluent condition. The permitting authority will then derive water 

quality-based effluent limits (WQBELs) and permit conditions based on the WQS variance and may set a 

schedule, if appropriate for attaining the WQBELs. States and authorized tribes have the discretion to 

set the term of the WQS variance according to the needs of the particular situation provided it is 

justified (see the preamble of the final rule for more discussion on setting the term of a WQS variance). 

See the section II. E of the preamble to the final rule and EPA’s response to code 8.f.ii – Variance 

Applicability – Permitting & 303(d) for more information about how WQS variances are implemented in 

NPDES permits. In addition, the final rule requires states adopting WQS variances applicable to a water 

body or waterbody segment to identify and document any cost-effective and reasonable best 

management practices (BMPs) for nonpoint sources (NPS) that could be implemented to make progress 

towards attaining the underlying designated uses. This provision is intended to encourage NPS controls, 

which many commenters correctly identified as important to improving water quality and ultimately 

attaining WQS. EPA does not agree with those comments that asserted that WQS variances will not lead 

to any NPS progress. For further discussion of how today’s rule addresses NPS to make environmental 

progress, see EPA’s response to code 8.g.v. – Variance Submission Requirements: Identification and 

Documentation of BMPs for NPS. 

A WQS variance is environmentally preferable to removing the designated use because the WQS 

variance is limited to a particular period of time, particular pollutants or pollutant parameters, and 

locations or dischargers. Instead of states or authorized tribes choosing to remove designated uses 

where the demonstration can be made that the designated use is not attainable due to at least one of 

the six factors listed in section 131.10(g) even in circumstances where the designated use is not 

attainable due to a single pollutant, states will now have more flexibility to utilize WQS variances.

Instead of removing the designated use, a WQS variance can provide a regulatory mechanism to retain 

the designated use by providing time-limited relief to the discharger for the one pollutant that includes 

requirements to reduce pollutant loads to the water body. For, example, whereas prior to this 

rulemaking a state or authorized tribe may have felt pressure from a discharger to remove a designated 

use because the discharger would be unable to comply with a WQBEL for a particular pollutant due to 

the substantial and widespread social and economic impacts it would have created, that state or tribe 

will have a WQS variance option that may provide the sought after relief.

In addition, the listing of waters as impaired under CWA section 303(d), and subsequent development 

and implementation of total maximum daily loads (TMDLs) for those waters, remain important 

regulatory tools to make progress toward attaining designated uses. While WQS variances affect the 

development of WQBELs for the discharger(s) specified in the WQS variance and are intended to 

support restoration, they do not affect the underlying designated use and criterion that apply to the rest 

of the water body. That is, WQS variances do not change the long term goals for the water body. TMDLs, 

on the other hand, are developed to achieve the long term goals of the water body and are thus based 

on the underlying designated use. Because the purposes of these two tools are different, milestones for 

progress in a WQS variance are not a replacement for establishing a TMDL for impaired waters. 

However, where WQS variances are approved for multiple dischargers on the same impaired water (or 

there is an approved WQS variance applicable to a water body or waterbody segment) and development 

of a TMDL is projected, the state/tribe has some flexibility to consider the relative priority of that 

particular TMDL while incremental progress is made through the variance(s). See EPA’s response to code 

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8.f.ii – Variances Applicability – Approved Variances and Permitting and 303(d) for additional discussion 

regarding TMDLs, CWA section 303(d) listing, and WQS variances.

One commenter expressed frustration with several perceived means of avoiding water quality-based 

pollutant controls and wondered why EPA felt WQS variances were under-utilized in this overall context. 

The progress EPA seeks is a clear path to achieving attainable improvements in water quality, and the 

WQS variance process can be a mechanism for both identifying what is attainable and implementing 

subsequent controls

D. Setting Standards for Unattainable Criteria

In contrast to the commenters above who believe that utilization of WQS variances will fail to lead to 

water quality improvements and attainment of designated uses because not enough is being done to 

force discharger progress, different commenters suggest (or imply) that utilizing WQS variances will, 

instead, lead to a more widespread application of “unattainable” standards for which there is no existing 

technology available. EPA disagrees with the conclusion that at least one commenter reaches, that the 

likelihood that unattainable standards will become more widespread because WQS variances will not 

hold up against legal challenges. This rulemaking is, in fact, intended to strengthen a state’s or 

authorized tribe’s ability to utilize WQS variances when duly adopted consistent with the requirements 

of the rule. The goal of the CWA is to restore and maintain the chemical, physical, and biological 

integrity of the Nation’s waters. The purpose of a WQS variance is to allow states and authorized tribes 

to make incremental progress toward attaining designated uses that are not currently attainable but 

may be attainable in the future. When used appropriately, WQS variances can provide a regulatory 

mechanism to improve water quality when a designated use cannot be attained in the near term, but a 

state or tribe wants to maintain the designated use as a long term goal.

In regards to the statement that WQS variances will lead to the application of “unattainable standards” 

because there is no existing technology available, EPA disagrees. The lack of technology to treat or 

remove a pollutant in a wastewater discharge to levels necessary to meet applicable WQS in and of itself

does not justify continuation of the discharge. EPA’s regulation provides a clear basis by which a state or 

authorized tribe can justify that a designated use is not attainable. If there is a concern that the 

designated use cannot be attained because there is no existing technology to meet the required WQBEL 

derived from the WQS, then the state or authorized tribe could evaluate, for example, whether there 

would be a substantial and widespread economic and social impact if the facility were to close because 

it cannot obtain or comply with an NPDES permit. Where the state or authorized tribe can show that 

there would be a substantial and widespread economic and social impact, then a WQS variance may be 

justified and approvable if all the other requirements of EPA’s regulation are met.

E. Other

Infrastructure Funding

Comments asserting that infrastructure funding would not be available if a discharger receives a WQS 

variance do not provide support for such claims. EPA knows of no reason why it would necessarily be 

the case that WQS variances would impact the availability of infrastructure funds. As mentioned in 

subsection B of this Essay, EPA estimates the burden and cost of revising variance policies in its EA of 

this final rule which can be found in docket number EPA–HQ–OW–2010–0606. 

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Water Quality Standards Variances and the Permit as a Shield

EPA disagrees with commenters asserting that a WQS variance eliminates the shield provided by an 

NPDES permit. A WQS variance is an interim WQS that is implemented through the NPDES permit and 

serves as the basis for WQBELs and permit conditions. Once an NPDES permit is issued, the permittee

would have the protections that are provided pursuant to CWA section 402(k) and section 122.5(a) of 

the NPDES permitting regulations if the permittee complies with all of the terms and conditions in its 

NPDES permit. The final rule does not address the legal shield a permittee obtains through an NPDES 

permit. 

Variances are “Regulatory in Nature”

EPA does not agree with the commenter that asserts that WQS variances are not “regulatory in nature.” 

As discussed in subsection A of this essay, EPA’s longstanding position is that individual WQS variances 

are revisions to WQS, which are legally binding, and require EPA review and approval. The commenter

suggests that EPA contradicts itself by asserting that EPA’s previous rulemaking indicated that 

regulations pertaining to WQS variances are not necessary because WQS variances are not “regulatory 

in nature.” Although EPA disagrees with the comment that the Agency is contradicting itself, the 

commenter is correct in that EPA did not finalize proposed regulations establishing requirements for 

WQS variances (47 FR 49234, October 29, 1982). When EPA finalized its 1983 rule, EPA affirmed many of 

the basic concepts of a WQS variance articulated in today’s final rule, but the Agency’s view in 1983 was 

that reliance on the existing regulations (as discussed in the 1977 OGC decision) provided sufficient 

regulatory basis for issuance of WQS variances. 

In particular, the preamble to the 1983 final rule (48 FR 51403, November 8, 1983), explained that “EPA 

has approved State-adopted variances in the past and will continue to do so, each individual variance is 

subject to public review, each WQS variance must be based on a demonstration... and that EPA will 

review for approval individual variances, not just an overall State variance policy.” These policy 

positions, along with the 1977 OGC decision formed the basis for EPA’s review and approval of WQS 

variances in the intervening years. Since the 1983 rulemaking, WQS variances have been underutilized. 

As explained in the preamble of the proposed rule (78 FR 54531, September 4, 2013) EPA has heard 

from states, tribes, and stakeholders that there is confusion, inconsistency, and mixed interpretations 

about how, when, and where WQS variances may be used appropriately. EPA now concludes that 

specifying requirements for WQS variances in regulation will encourage the utilization of WQS variances 

by providing greater regulatory certainty, national consistency and transparency to the WQS variance 

process. Therefore, with the final rule at section 131.14 the Agency is exercising its authority under CWA 

section 501(a) to prescribe such regulations EPA determines as are necessary to carry out the CWA. 

Suggested Changes to Title 40 of the Code of Federal Regulation Section 131.20(a)

EPA addresses the comments regarding suggested changes to 40 CFR 131.20(a) in Essays 6.e, 6.f, and 

6.g.

Technology-Based Limits

With regard to comments on technology-based limits, see EPA’s response in Essay 8.f.iii.

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Essay 8.c – Variances: Proposed Definition

A. General

The U.S. Environmental Protection Agency’s (EPA’s) final rule defines a “water quality standards 

variance” (WQS variance) as a time-limited designated use and criterion for a specific pollutant(s) or 

water quality parameter(s) that reflect the highest attainable condition (HAC) during the term of the 

WQS variance. The definition encompasses both discharger(s)-specific WQS variances and WQS 

variances to a water body or waterbody segment. In the final rule, EPA has clarified the different 

requirements for these two types of WQS variances. See Response Essay 8.f.i for more discussion on the 

distinction between types of WQS variances and a discussion of EPA’s authority to allow WQS variances 

for a water body or waterbody segment. See section II.E of the final rule preamble for a full discussion 

on EPA’s legal authority related to WQS variances as well as Response Essay 8.m.

EPA acknowledges the support for the proposed definition. Based on comments, EPA revised the 

proposed definition in the final rule to make EPA’s intended meaning clearer. The final rule definition 

clarifies that EPA allows WQS variances for water quality parameters (e.g., dissolved oxygen) in cases 

where the water quality parameter may not be considered a “pollutant.” The rule also clarifies that the 

“specified time period” described in the proposed rule is the “term of the WQS variance.”

B. Highest Attainable Condition

EPA disagrees with the commenter that suggested the HAC for a WQS variance is same as “highest 

attainable use” (HAU), and that EPA should include a definition of HAC in rule. The HAU is explicitly 

defined in section 131.3(m) as “the modified aquatic life, wildlife, or recreation use that is both closest 

to the uses specified in section 101(a)(2) of the Act and attainable, based on the evaluation of the 

factor(s) in § 131.10(g) that preclude(s) attainment of the use and any other information or analyses 

that were used to evaluate attainability...” In contrast, EPA has explained in guidance that it considers 

the term HAC to mean “the condition that is both feasible to attain and is closest to the protection 

afforded by the designated use and criteria.” 1

 The HAU applies only to Clean Water Act (CWA) section 

101(a)(2) uses and subcategories of such uses and must be determined by a use attainability analysis 

(UAA) using at least one of the six factors specified in section 131.10(g) and other information used to 

evaluate attainability. The HAC, however, applies to a WQS variance for either 101(a)(2) or non101(a)(2) uses2 and is used to form the basis of the interim requirements of the WQS variance. EPA 

concluded that, for WQS variances, identification of the HAC is appropriate regardless of whether or not 

the WQS variance is to uses specified in CWA section 101(a)(2) (or subcategories of such uses) or to non101(a)(2) uses. This is because for WQS variances, unlike a “permanent” change to the designated use, 

the state or authorized tribe has intentionally made the decision to keep pursuing progress toward 

achieving the underlying WQS and identifying the HAC is a measurable step to ensure progress is made. 

See response essay 5.h. for discussion about non-101(a)(2) uses. Further, it is not necessary for EPA to 

 

1 http://water.epa.gov/scitech/swguidance/standards/upload/Discharger-specific-Variances-on-a-Broader-ScaleDeveloping-Credible-Rationales-for-Variances-that-Apply-to-Multiple-Dischargers-Frequently-Asked-Questions.pdf 2 The final rule at section 131.3(q) defines “non-101(a)(2) use” as any use unrelated to the protection and 

propagation of fish, shellfish, wildlife or recreation in or on the water.

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provide a formal definition of HAC in the final rule because the final requirements at 

section 131.14(b)(1)(ii) outline the options available to a state or authorized tribe to articulate the HAC. 

See the options available to states and authorized tribes to articulate the HAC for a discharger(s)-specific 

WQS variance at section 131.14(b)(1)(ii)(A) and for a WQS variance applicable to a water body or

waterbody segment at section 131.14(b)(1)(ii)(B).

States and authorized tribes are not required to identify the HAC through a UAA, although such an 

analysis could be helpful. However, the final rule at section 131.14(b)(2)(i) does require states and 

authorized tribes to submit a WQS variance with supporting documentation to justify the adoption of a 

WQS variance. For a WQS variance to a 101(a)(2) use, states and authorized tribes must include a

demonstration that the use and criterion are not feasible to attain based on one of six factors in 

section 131.10(g), or a new factor related to lake, stream, or wetland restoration specified at 

section 131.14(b)(2)(i)(A)(2). For a WQS variance to a non-101(a)(2) use, states and authorized tribes 

must include documentation justifying how the state or authorized tribe considered the use and value of 

the water for those uses listed in section 131.10(a) and appropriately supports the justification for the 

WQS variance and its term. See also Response Essay 8.g.iv for a discussion on WQS variances to non101(a)(2) uses. See also Response Essay 8.g.iii and section II.E, subsection “What is EPA’s Position on 

Certain Public Comments?” in the preamble to final rule for additional discussion on the comparison of 

the level of rigor related to WQS variances as compared to UAAs required for changes to 101(a)(2) uses.

EPA disagrees with commenters suggesting that EPA should include in the definition of a WQS variance

language that specifies the HAC as the “condition during the specified time period that the State 

determines is highest attainable.” A WQS variance is a new or revised WQS subject to EPA review and 

approval or disapproval, requires a public process for adoption, and must be reviewed by the state or 

authorized tribe on a triennial basis. The CWA assigns EPA an oversight role of reviewing and approving 

or disapproving state and authorized tribal WQS (CWA section 303(c)). Specifying in the rule that the 

HAC is what “the State determines is highest attainable” is inconsistent with the oversight role provided 

in the CWA. See also response below to comments suggesting that the rule should not define a WQS 

variance as a WQS subject to EPA review and approval.

EPA agrees with comments stating that the definition of HAC should include a requirement “...to specify 

and verify the highest achievable water quality possible during the term of the variance.” The definition 

of a WQS variance in the final rule at section 131.3(o) does not stand alone. The final rule at 

section 131.14 specifies the information states and authorized tribes must submit to EPA for any WQS 

variance, including interim requirements that reflect the HAC, and supporting documentation justifying 

the WQS variance term.

C. Water Quality Standards Variances are Water Quality Standards

EPA does not agree with comments suggesting the deletion of the regulatory text from section 131.14 

that pertains to EPA’s position that WQS variances are WQS subject to EPA review and approval or 

disapproval. The legal basis and reasons why a WQS variance is a WQS are set forth in detail in Response 

Essay 8.f.i. In addition, for the reasons set forth in Response Essay 8.f.i, EPA does not agree with the 

commenter who requests that EPA consider individual WQS variances as not to be WQS similar to 

individual compliance schedules (CS) which EPA does not consider to be WQS. A CS for water qualitybased effluent limits (WQBELs) in National Pollutant Discharge Elimination System (NPDES) permits is

specified in the permitting regulation at section 122.47 and is not itself a WQS. The final rule does not 

modify any permit CS requirements specified at section 122.47. In addition, as described in section II.F of 

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the preamble for the final rule, EPA has streamlined the regulatory text related to compliance schedule 

authorizing provisions (CSAPs) to clarify that, although a CSAP is a WQS, a CS itself is not a WQS. See 

Response Essay 8.e for additional discussion on the distinction between CS and WQS variances.

For the same reasons discussed above, EPA also does not agree with the commenter who suggests 

language so that only variance policies and procedures are considered WQS subject to EPA review and 

approval or disapproval. See also Response Essay 8.f.i for a discussion on why a WQS variance itself is a 

WQS subject to EPA action under CWA section 303(c).

D. Effective Date

In response to comments related to deletion/inclusion of language in regulatory text as proposed: “Any 

such WQS variances adopted after [effective date of the final rule] must be consistent with this 

regulatory section,” EPA is no longer including such language in the final rule text. Instead, EPA 

describes, in section I.E, “When Does this Action Take Effect?” and in section II.E, subsection “What is 

EPA’s Position on Certain Public Comments?,” the Agency’s position on when the regulations are 

effective in general and additional discussion related to existing or future WQS variances as well as state 

and authorized tribal WQS variance policies and procedures.

EPA also notes that any WQS variance that is submitted after the final rule is in effect must be approved 

under CWA section 303(c) before it is the applicable WQS for CWA purposes. EPA’s regulations were 

revised in April 2000 (65 FR 24653; April 27, 2000) to clarify that WQS adopted after May 30, 2000 did 

not become the applicable WQS for CWA purposes until EPA approves such WQS. See Response Essay

8.f.i for discussion on why it is important for the time-limited WQS variance to be recognized as the 

applicable WQS for the specified CWA purposes (e.g., NPDES permitting).

E. Adaptive Management Approach

In response to comments asking for EPA to be forthcoming or define what “adaptive management 

approaches,” EPA expects states and authorized tribes to implement, EPA notes that the Agency is not 

requiring “adaptive management approaches” as part of the final rule and EPA has therefore concluded 

that it is not necessary for the rule to contain such a definition. As described in the preamble to 

proposed rule, one of the stated purposes of a WQS variance is to allow time to implement adaptive 

management approaches that make progress towards attaining the underlying designated use and 

criterion. Adaptive management is a concept generally recognized as exploring alternative ways to meet 

management objectives, predicting the outcomes of alternatives based on the current state of 

knowledge, implementing one or more of these alternatives, monitoring to learn about the impacts of 

management actions, and using the results to update knowledge and adjust management actions.3 EPA 

believes that adaptive management can be useful in the context of a WQS variance because it involves 

continuous feedback between the interpretation of new information and management actions that can 

be key to targeting actions where they will actually be effective.

 

3 Murray, C. and D.R. Marmorek. 2004. Adaptive management: A science-based approach to managing ecosystems 

in the face of uncertainty. In: N.W.P. Munro, T.B. Herman, K. Beazley and P. Dearden (eds.). Making Ecosystembased Management Work: Proceedings of the Fifth International Conference on Science and Management of 

Protected Areas, Victoria, BC, May, 2003. Science and Management of Protected Areas Association, Wolfville, Nova 

Scotia (as cited in the U.S. Department of Interior’s Technical Guide: Adaptive Management, 2009 edition).

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An adaptive management approach for a WQS variance should involve a discernible sequence of specific 

actions with the potential to achieve the underlying designated use and criterion. Each step in the 

process should inform or be a necessary predecessor to the next set of decisions to make progress 

towards the underlying designated use and criterion. In addition, each step in the process should 

conform to generally accepted timeframes for implementing and evaluating each management action

(i.e., there should be no unjustified periods of time that do not involve planning an action, implementing 

an action, or evaluating the outcome of an action). 

F. Including Both “Designated Use” and “Criterion” in the Definition

Commenters expressed concern regarding WQS variances as being defined as a “time-limited 

designated use and criterion.” Commenters suggest that dischargers only have difficultly complying with 

a criterion for a particular pollutant and that EPA’s inclusion of designated uses in the definition of a 

WQS variance confuses WQS variances with use changes under section 131.10. Commenters agree with 

EPA that a WQS variance should maintain the underlying use and criterion as the applicable WQS for 

other dischargers, for waterbody assessment, and for total maximum daily load (TMDL) development. 

Commenters suggest that use changes or site-specific criteria should be used when the situation is not 

discharger or pollutant specific.

After consideration of comments, EPA did not remove the term “designated use” from its definition of 

WQS variance. The purpose of ambient water quality criteria, as set forth in sections 131.2, 131.6 and 

131.11, is to protect designated uses. EPA agrees with commenters that dischargers often desire a WQS 

variance because they have difficulty complying with a criterion for a particular pollutant. However, 

adopting a less stringent criterion would no longer protect the underlying designated use as required by 

sections 131.2, 131.6 and 131.11. EPA cannot dissociate the concepts of criteria and the designated uses 

they protect. Thus, an important legal construct for a WQS variance is that it provides for a revised 

(usually less stringent) criterion or criteria that protects a revised designated use for a limited amount of 

time. EPA notes that if a revised criterion continues to protect the underlying use, the state could 

instead adopt and seek approval of a site-specific criterion.

To address potential confusion about how designated uses relate to WQS variances, EPA modified the 

way states and authorized tribes must articulate the interim requirements of a WQS variance. First, EPA 

separates the requirements for WQS variances to individual dischargers and WQS variances for a water 

body or waterbody segment, and expressly provides states and authorized tribes the option for 

dischargers to describe the HAC without the need to articulate a time-limited designated use

(section 131.14(b)(1)(ii)(A)). This separation allows EPA to retain the requirement that states and 

authorized tribes articulate both a time-limited designated use and criterion when the scope of the WQS 

variance pertains to entire water body or waterbody segment because EPA recognizes the importance of 

identifying a time-limited designated use when a WQS variance applies to an entire water body or 

waterbody segment (section 131.14(b)(1)(ii)(B)). See section II.E. of the preamble to the final rule for 

EPA’s rationale for the regulatory options provided at section 131.14(b)(1)(ii)(A) and (B). 

With regard to concerns about the applicability of the underlying use and criterion during the term of a 

WQS variance, EPA’s final preamble and rule clarifies that the time-limited designated use and criterion 

applies only for purposes of developing NPDES permit limits and requirements under 301(b)(1)(C), and 

for issuing certifications under CWA section 401. States and authorized tribes must retain the underlying 

designated use and criteria in their standards (see section 131.14(a)(2) and (3)). Taken together, these 

two provisions mean that states and authorized tribes must continue to use the underlying designated 

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use and criterion for other CWA purposes such as assessing attainment of designated uses, listing waters 

as impaired under CWA section 303(d), and developing TMDLs, even with an EPA-approved WQS 

variance regardless of the scope of the WQS variance.

In response to the commenter’s suggestions that WQS variances are not appropriate for a larger scope 

(e.g., WQS variances applicable to a water body or waterbody segment) see Response Essay 8.f.i.

G. Use of Water Quality Standards Variances Should Be “Sunsetting” 

EPA appreciates commenters’ support for the proposed WQS variance definition. However, EPA 

disagrees with commenters who suggest that use of WQS variances should be “phased out.” As 

described in section I.C of the preamble to the final rule, pollutants from large-scale land use changes, 

extreme weather events, or environmental stressors related to climate change can hinder restoration 

and maintenance of water quality. In addition, pollutants can be persistent in the environment and, in 

some cases, lack economically feasible control options. These challenges necessitate a more effective, 

flexible, and practicable approach to meeting the WQS objectives of the CWA. States and authorized 

tribes can use WQS variances to make progress toward attaining designated uses when they are not 

attainable or where there is uncertainty about the designated uses that are attainable. This final rule 

creates a regulatory framework that ensures states and authorized tribes use WQS variances 

appropriately and effectively to address difficult water quality challenges.

H. Needing to “Comply” with the Definition and Changes to What Is Required

EPA disagrees with the commenter who asserts that if the “discharger has otherwise demonstrated 

entitlement to a variance for the reasons specified under existing state rules or 40 CFR § 131.10(g), for 

example, then there should be no need to insist upon compliance with these definitions.” See section 

II.E of the preamble of the final rule and Response Essay 8.m for discussion of EPA’s legal authority with 

regard to WQS variances. The discussion includes the rationale for why a WQS variance is time-limited 

and how the construct of the “highest attainable condition” enables water bodies to serve the objective 

of the Act to restore and maintain the chemical, physical, and biological integrity of the Nation’s waters. 

EPA disagrees with commenters claiming a discharger (or state or authorized tribe) can demonstrate 

“entitlement to a variance for reasons specified under existing state rules.” See response to comments 

explaining why all WQS variances are WQS subject to EPA review and approval or disapproval under 

CWA section 303(c). States and authorized tribes may adopt a WQS variance policy that is more 

stringent than the regulatory requirements under section 131.14 (see also discussion section IV. E and 

section II.E, subsection “What is EPA’s Position on Certain Public Comments?” in the preamble to the 

final rule about when and how states and authorized tribes may need to reevaluate and/or revise their 

WQS to comply with this final rule). EPA agrees with the comment that states and authorized tribes do 

not need to have their own explicit WQS variance authorization provision, policy or procedure to adopt 

and submit WQS variances to EPA for review and action.

EPA disagrees with comments asserting that the definition of a WQS variance no longer requires a 

variance to be “adopted consistent with the substantive and procedural requirements for downgrading 

a designated use.” Although not specified in the definition of a WQS variance at section 131.3(o), the 

final rule at section 131.14(b)(2) restricts the justification for WQS variances to essentially the same

factors that must be used to justify removal of designated uses. For uses specified in 101(a)(2) of the 

Act, section 131.14(b)(2)(i)(A) requires states or authorized tribes to demonstrate that the underlying 

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designated use is not attainable on the basis of at least one of the factors specified in section 131.10(g) 

(or an additional factor related to waterbody restoration specified in section 131.14(b)(2)(i)(B)). For uses 

not specified in section 101(a)(2) of the Act, section 131.14(b)(2) requires a state or authorized tribe to

demonstrate how its consideration of the use and value of the water for those uses listed in 

section 131.10(a) appropriately supports the WQS variance and term. 

The explanation in the 1977 Office of General Counsel’s memorandum that the commenter references 

explains that a WQS variance is “environmentally preferable” to permanently downgrading the standard 

for the entire stream. In this statement “the standard” is the use and all the criteria adopted and 

approved to protect that use. The memorandum explains that a WQS variance is narrower in that, even 

for a particular discharger, the variance only applies to the particular constituent, the underlying 

standard is in place for all other criteria, and the WQS variance is only for a limited time. EPA’s 

application of WQS variances to a water body or waterbody segment is consistent with the rationale in 

the memorandum. The application is still limited to the pollutant(s) at issue and is still time-limited. EPA 

notes that in addition to finalizing a formal definition of “WQS variance” in section 131.3(o), EPA has 

also included several provisions that are specific to this type of WQS variance (see section

131.14(b)(2)(iii)) to ensure increased transparency and accountability. Finally, it is worth noting that the 

1977 OGC memorandum was issued interpreting the then current WQS regulations and how a state may 

decide to adopt a WQS variance consistent with those regulations. In this new rulemaking, EPA is 

promulgating a set of regulatory requirements specifically for variances. See also Response Essay 8.f.ii 

for a discussion of the use of WQS variances for purposes related to CWA section 401 certification.

EPA disagrees with the commenter that asserts the definition of a WQS variance should include a 

“requirement that the original water quality standard must be attained by a date certain.” As described 

in section II.E for the final rule, the purpose of a WQS is to allow a state or authorized tribe time to make 

progress toward meeting the “original” (or “underlying”) designated use and criterion. A WQS variance

can be particularly useful when a state or authorized tribe can make progress toward meeting the 

designated use and criterion, but the time required to attain the underlying designated use and criterion 

is uncertain. In such circumstances, the state or authorized tribe can adopt the HAC as the applicable 

WQS during the term of the WQS variance.

At the end of a WQS variance term, the state or authorized tribe can assess the feasibility of attaining 

the underlying WQS. If the state or authorized tribe determines that the underlying WQS is attainable 

but the permittee cannot immediately meet the WQBEL derived from the WQS, the permitting authority 

can decide whether to include a compliance schedule (CS) (where authorized) in the permit thereby 

providing time for the permittee to come into compliance with the effluent limits in its NPDES permit.

(See CWA section [502(17)] for a definition of “Schedules of compliance” and Title 40 of the Code of 

Federal Regulations (CFR) section 122.47). Any such CS must include a final effluent limit based on the 

underlying WQS and must require compliance with the permit’s WQBEL “as soon as possible.” In many

cases, EPA expects that states and authorized tribes will identify a HAC for a WQS variance that is short 

of full attainment of the underlying designated use and criterion. When such a WQS variance expires, 

the state or authorized tribe can assess the attainability of the underlying designated use and criterion 

and either adopt another WQS variance using the new (more stringent) HAC, or it can allow the 

underlying designated use and criterion to resume as the applicable WQS for the permittee.

EPA reminds the commenter that under the final rule the WQS variance applies only for purposes of 

developing NPDES permit limits and requirements under 301(b)(1)(C), and for issuing certifications 

under CWA section 401. The underlying designated use and criterion remain in place as the applicable 

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standard for all other CWA purposes including waterbody assessment under CWA sections 303(d) and 

305(b) and for TMDL development. EPA believes that the full set of requirements under section 131.14 

(e.g. requirements for reevaluation of the HAC through a public process) will ensure progress toward the 

underlying designated use and criterion while retaining the flexibility states and authorized tribes need 

to manage uncertainty when making progress toward attaining the underlying designated uses in 

challenging situations.

I. Thermal Variances

EPA agrees with the commenter that thermal variances satisfying section 316(a) are not subject to 

section 131.14 as finalized. EPA has clarified this point by including a definition specific to “WQS 

variances” in the final rule under section 131.3(o) so that the public do not confuse WQS variances with 

permitting variances. 

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Essay 8.d – Variances: Where Variances May/May Not be Useful

A. General Support

The U.S. Environmental Protection Agency (EPA) appreciates commenters’ support for the final rule.

B. Variances Should Only Be Allowed As a “Special Exception” or under 

“Exceptional” Circumstances

The commenter requested that water quality standards (WQS) variances should be granted only as a 

means to achieve the end of meeting the designated use and that WQS variances should be subject to 

scrutiny by EPA. EPA’s position is that the final rule is designed to, and will, accomplish what the 

commenter requested. The objective of authorizing the adoption of WQS variances is to provide time to 

improve water quality with the ultimate goal being to attain, if possible, the underlying WQS. All WQS 

variances must be submitted to EPA for review and approval.

The final rule provides for states and authorized tribes to utilize WQS variances in specific 

circumstances. For a WQS variance to a designated use specified in Clean Water Act (CWA) section 

101(a)(2) and subcategories of such uses, states and authorized tribes must demonstrate that the use 

and criterion are not feasible to attain on the basis of one of the factors listed in section 131.10(g), the 

same factors that could be justified to remove those designated uses. The final rule also includes a new 

restoration-related factor in section 131.14(b)(2)(i)(A)(2) so that states and authorized tribes may grant 

a WQS variance for environmental restoration projects such as removing a dam that will help restore 

water quality in the long term, but may temporarily result in nonattainment of WQS while the 

restoration project is active. For WQS variances to non-101(a)(2) uses, today’s rule specifies that states 

and authorized tribes must document and submit a use and value demonstration consistent with section

131.10(a) (see section II.B of the final rule for additional discussion on use and value demonstrations).

These limitations on WQS variances are generally analogous to the limitations for removing designated 

uses. Because a WQS variance is an interim designated use and criterion reflecting the highest attainable 

condition (HAC), applies only to specific pollutants or pollutant parameters, specific dischargers or water 

bodies, and for a specific amount of time, a WQS variance can be an environmentally preferable option 

to permanently removing a designated use. The final rule also requires states and authorized tribes to 

reevaluate variances longer than five years at least every five years, to include a provision in the WQS 

variance that any more stringent highest attainable use (HAU) later identified shall be the applicable 

WQS variance, and require states to include a provision in the WQS variance that the WQS variance shall 

no longer be the applicable WQS if the reevaluations do not take place as specified. Along with the 

requirement that EPA review and approve all WQS variance before they can be used for CWA purposes, 

EPA believes that final rule ensures WQS variances will be used appropriately and only in the specific 

circumstances outlined in section 131.14. 

C. EPA Should Allow State Flexibility Such as Multiple Discharger Variances

The final rule provides for a state or authorized tribe to adopt one WQS variance that applies to multiple 

dischargers so long as the WQS variance is consistent with the CWA and section 131.14. Multiple 

discharger WQS variances can serve as a significant administrative streamlining mechanism when used 

in situations where several dischargers are experiencing the same challenges in meeting their water 

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quality-based effluent limits (WQBELs) for the same pollutant. The preamble of the final rule discusses

how states and authorized tribes might structure a multiple discharger variance. EPA has also developed 

a list of frequently asked questions (FAQs) addressing when a multiple discharger WQS variance may be 

appropriate and how a state or authorized tribe can develop a credible rationale for this type of WQS 

variance (Discharger-specific Variances on a Broader Scale: Developing Credible Rationales for Variances 

that Apply to Multiple Dischargers, EPA-820-F-13-012, March 2013). The preamble of the final rule also 

discusses other ways for states and authorized tribes to streamline their WQS variance process such as 

adopting an administrative procedure that fulfills the WQS submittal and review requirements and 

specifies that if the state or authorized tribe follows the procedure, the WQS variance is legally binding 

under state or tribal law. The commenters should refer to the preamble of the final rule for more 

information.

D. Clarification on Use of a Variance When Natural Conditions Are a Cause of

Nonattainment of Water Quality Standards

A water body may not meet the criterion for a pollutant or pollutant parameter, but the state or 

authorized tribe may nonetheless believe the water body may be attaining the designated use. One 

possibility is that the criterion may be overly stringent due to site-specific factors. Another possibility is 

that the water body has an unusual concentration of the pollutant or pollutant parameter that is

naturally present in the water body. 

Natural condition is a term used to describe the quality of surface water untouched by human-caused 

pollution or disturbance. How a state or authorized tribe determines whether or not a natural condition

affects attainment of a WQS is beyond the scope of the final rule. In such a circumstance, a WQS 

variance would generally not be the appropriate long-term tool to address criterion exceedance because 

such a condition is unlikely to change whereas the WQS variance is time-limited. The intent of a WQS 

variance is to make incremental progress toward attaining the underlying designated use when the

underlying designated use is not attainable in the near term but may be attainable in the future. If the 

state or authorized tribe has compelling evidence that natural conditions prevent attainment of the 

designated use but is uncertain about the possible extent of human-caused contribution, the state or 

authorized tribe may choose to adopt a short-term (e.g., 5 years or less) WQS variance to provide time 

to perform the studies necessary to identify the contributors to the criterion exceedances and more 

definitively determine whether or not the designated use is attainable over the long-term. If, based on 

the evidence from the studies, a state or authorized tribe concludes the water body exceeds the 

criterion due to a natural conditions, the state or authorized tribe may choose to account for the natural 

condition by modifying the designated use based on section 131.10(g)(1) because the natural condition 

is unlikely to change. If studies demonstrate that the water body is attaining the designated use despite 

exceedance of the current criterion, the state or authorized tribe may instead choose to develop a sitespecific criterion that accounts for the unique characteristics of the water body. EPA has developed 

technical materials to aid states and authorized tribes in developing scientifically defensible natural 

conditions-based site-specific criteria for temperature, dissolved oxygen and pH 

(http://water.epa.gov/scitech/swguidance/standards/library/upload/natural-conditions-framework2015.pdf). EPA disagrees with the commenter that requests that a WQS variance be used “to allow 

further excursion of the criterion beyond the natural condition if uses can still be protected.” First, if the 

state or authorized tribe identifies the natural condition correctly, that will be the level at which the 

“uses can still be protected.” A less stringent level would not be protective. Second, section

131.14(b)(1)(ii) prohibits the requirements of a WQS variances from lowering currently attained water 

quality (with one exception related to the factor associated with dam removal and wetland, lake, or 

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stream restoration). Therefore, if the water body is currently achieving the water quality associated with 

the natural condition, then the state or authorized tribe cannot identify a less stringent level as the HAC

for the term of the WQS variance.

E. EPA Should Specify That Seasonal Water Quality Standards Variances Are 

Allowed

The final rule does not preclude a seasonal WQS variance. Rather than specify all scenarios where a 

WQS variance may be acceptable, EPA chose to specify in regulation the minimum requirements of a 

WQS variance. EPA believes that specifying the basic requirements of a WQS variance in this final rule 

provides national consistency and accountability for WQS variances while providing states and 

authorized tribes the flexibility needed to address their unique water quality challenges.

F. Should Only Allow Variances to Make Progress, Not Let Permittees Delay 

Meaningful Progress

EPA agrees with comments indicating that a WQS variance should be used to make feasible progress 

towards attainment of designated uses and not to “let permit holders indefinitely defer or delay 

meaningful progress towards attainment.” The final rule includes several provisions to ensure states and 

authorized tribes use WQS variances to make feasible progress toward achieving designated uses. The 

final rule requires a WQS variance to include interim requirements representing the HAC of the water 

body or waterbody segment applicable throughout the term of the WQS variance in a quantifiable 

manner. The final rule requires states and authorized tribes to include in a WQS variance a statement 

providing that the requirements of the WQS variance are either the HAC identified at the time of the 

adoption of the WQS variance, or the HAC later identified during any reevaluation whichever is more 

stringent. The final rule requires that any WQS variance with a term greater than five years specifies a 

reevaluation frequency no less frequently than every five years, requires the results of the reevaluation 

to be submitted to EPA within 30 days, and requires the WQS variance to contain a provision that the 

WQS variance will no longer be the applicable WQS if those requirements are not fulfilled. The final rule 

specifies the factors that states and authorized tribes may use to justify the need for a WQS variance, 

and requires states and authorized tribes to justify the term of the WQS variance by describing the 

pollutant control activities needed to achieve the HAC. For a waterbody variance, the final rule further 

requires identification and documentation of any cost-effective and reasonable best management 

practices (BMPs) for nonpoint source (NPS) controls related to the pollutant(s) or water quality 

parameter(s) and water body or waterbody segment(s) specified in the WQS variance that could be 

implemented to make progress towards attaining the underlying designated use and criterion, and in 

the case of any subsequent waterbody variance, documentation of whether and to what extent BMPs

were implemented to address the pollutant(s) or water quality parameter(s) subject to the WQS 

variance and the water quality progress achieved. Finally, the final rule, specifies that any limitations and 

requirements necessary to implement the WQS variance shall be included as enforceable conditions of 

the National Pollutant Discharge Elimination System (NPDES) permit for the permittee(s) subject to the 

WQS variance. The EPA believes that these provisions in the final rule will ensure that WQS variances 

are used appropriately. For comments concerning the length of a WQS variance, see response essay 

8.g.iii.

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G. Must Require EPA Review and Approval

EPA also agrees with commenters indicating that EPA should review requests for a WQS variance. A 

WQS variance is itself a WQS subject to EPA review and approval or disapproval. See response essay 8.f.i

for further discussion.

H. New Dischargers

Commenters suggest the final rule should specify the types of “new dischargers” eligible to receive a 

WQS variance. However, the commenters do not specify the meaning of the term “new discharger.” The 

term “new discharger” is currently defined in the NPDES permitting regulations at section 122.21 with 

respect to the date EPA published the relevant industry effluent guidelines. Assuming the commenters 

intend the term “new discharger” to mean a potential discharger that has never previously discharged 

under an NPDES permit but will commence discharging under a new NPDES permit, the final rule does 

not prohibit a state or authorized tribe from granting a WQS variance to such a discharger provided the

WQS variance fulfills the requirements of the final rule at section 131.14. The final rule specifies that a 

WQS variance shall not result in any lowering of the currently attained ambient water quality, unless it

is temporarily necessary for restoration activities that facilitate lake, wetland, or stream restoration 

through dam removal or other significant reconfiguration activities consistent with section

131.14(b)(2)(i)(A)(2)). EPA included this provision in the final rule to allow long-term water quality 

improvement even in situations that may require short-term lowering of water quality. EPA disagrees

with commenters suggesting that the final rule specify the specific types of “new dischargers” eligible to 

receive a variance because EPA cannot reasonably anticipate all the types of “new dischargers” that may 

be eligible for a WQS variance under these circumstances. See also response to Essay 8.f and 8.f.i. 

I. There Are Too Many Requirements Making Water Quality Standards

Variances More Burdensome than Permanently Removing the Designated Use

EPA disagrees with commenters suggesting that the requirements for a WQS variance are more 

burdensome than the requirements for permanently removing a designated use and thus a disincentive 

for using WQS variances. These commenters assert that permanently removing a designated use would 

only require demonstration that at least one of the factors listed in section 131.10(g) applies, whereas a 

WQS variance would require a similar demonstration, while additionally requiring the setting of the 

highest attainable interim use and interim numeric criterion, or interim numeric effluent condition, and

is limited to ten years. 

EPA disagrees that adopting a WQS variance is more burdensome than permanently removing a 

designated use. To remove a designated use, states and authorized tribes must demonstrate that the 

designated use is not attainable through a use attainability analysis (UAA). A UAA is a structured 

scientific assessment of the factors affecting the attainment of the use that may include physical, 

chemical, biological, and economic factors as described in section 131.10(g). If the state or authorized 

tribe finds through the UAA that the designated use is not attainable, the state or authorized tribe may 

 

1 New discharger means any building, structure, facility, or installation: (a) From which there is or may be a 

‘‘discharge of pollutants;’’ (b) That did not commence the ‘‘discharge of pollutants’’ at a particular ‘‘site’’ prior to 

August 13, 1979; (c) Which is not a ‘‘new source;’’ and (d) Which has never received a finally effective NDPES 

permit for discharges at that ‘‘site.’’

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remove the designated use, but must adopt in its place the HAU and all criteria necessary to protect the 

HAU. Unlike removing a designated use, however, states and authorized tribes typically grant a WQS 

variance to a single discharger for only one or a few pollutant parameters for a limited period of time. As 

described in section II.E of preamble to the final rule, EPA recognizes that the data and analyses often 

needed to support adoption of a WQS variance could be less complex and require less time and 

resources compared to removing a designated use because many WQS variances evaluate only one 

parameter for a single permittee for a limited period of time. Thus, demonstration of the need for a

WQS variance and identification of the HAC can be significantly less burdensome than conducting a 

UAA. Furthermore, the final rule reduces administrative burden associated with utilization of WQS 

variances by eliminating the 10-year term limit that was specified in the proposed rule. The final rule 

provides states and authorized tribes with the discretion to determine the necessary WQS variance term 

provided it is unambiguously identified as part of the WQS variance and the state or authorized tribe has 

sufficiently justified the need for the variance consistent with the documentation the state or authorized 

tribe must submit to EPA. EPA believes that in the vast majority of cases, adopting a WQS variance is 

likely to be substantially less burdensome than permanently removing a designated use, and provides 

states and authorized tribes with needed flexibility in their WQS program to keep as a long-term goal 

designated uses that are not immediately attainable while making progress toward achieving them.

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Essay 8.e – Variances: Variances versus Compliance Schedules

A. The Rule Should Prohibit Compliance Schedules for Meeting Water QualityBased Effluent Limits in a National Pollutant Discharge Elimination System

Permit Derived from a Variance

The U.S. Environmental Protection Agency (EPA) thanks commenters who support the EPA’s discussion 

in the preamble to the proposed rule regarding when it is appropriate to use water quality standards 

(WQS) variances and permit compliance schedules (CS) and agrees EPA’s interpretation is consistent 

with the “Hanlon Memo” of May 10, 2007.

EPA disagrees with commenters that said EPA should prohibit CS when meeting water quality-based 

effluent limits (WQBELs) in a National Pollutant Discharge Elimination System (NPDES) permit derived 

from a WQS variance. A WQS variance and a permit CS serve different purposes. The rule defines a WQS 

variance at section 131.3(o) as a time-limited designated use and criterion for a specified pollutant(s), 

permittee(s), and/or water body or waterbody segment(s) that reflects the highest attainable condition 

(HAC) applicable throughout the specified time period. As discussed in section II.E of the preamble to 

the final rule, where a permittee cannot immediately meet the WQBEL derived from the terms of a WQS 

variance, the permitting authority has the discretion to decide whether to provide a permit CS

(assuming the state or authorized tribe has a provision authorizing the use of CS in such circumstances) 

providing time for the permittee to come into compliance with its WQBEL.

1 (See Clean Water Act [CWA] 

section [502(17)] for a definition of “schedules of compliance” and Title 40 of the Code of Federal 

Regulations [CFR] section 122.47).2

 Such schedules of compliance must lead to compliance with the 

effluent limits derived from the WQS variance “as soon as possible.”

The regulation at section 122.47 provides for CS because in some cases a permittee cannot reasonably 

be expected to immediately meet a WQBEL if meeting the WQBEL requires installation or upgrading of 

treatment facilities. Similarly, it may not be reasonable to expect a permittee to immediately meet a 

more stringent WQBEL based on the HAC of a WQS variance if meeting the WQBEL requires installation 

or upgrading of treatment facilities. In either case, the use of a CS must lead to compliance with the 

WQBEL as soon as possible. Any CS for a WQBEL derived to meet an interim WQS in a WQS variance will 

need to meet the same requirements as any other CS for a WQBEL. One comment stated that allowing a 

WQS variance for a pre-1977 WQS undermines the principle in Star-Kist against authorizing a CS for 

WQBELs based on pre-1977 standards. The adoption of a WQS variance as an interim use and criterion

(or HAC) changes the WQS, just as a permanent use downgrade, and WQBELs appropriately must be 

based on the applicable WQS. In the case of a WQS variance, the applicable WQS is the interim use and 

criterion (or HAC) in the WQS variance. This does not undermine the principle in Star-Kist. Rather, it 

applies and implements the established CWA and NPDES permitting requirements to base WQBELs on 

the applicable WQS.

 

1 As an alternative to a permit CS, there may be other available mechanisms such as an administrative order. 2 78 Fed. Reg. 54532 (September 4, 2013).

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The preamble to the final rule provides an example of when and how both tools could be used together 

to provide time to a discharger to meet the HAC of its WQS variance. Additionally, the final rule does not 

give preference to one tool over the other, as some commenters requested, as WQS variances and CS

are different tools intended for different situations. See the discussion in the preamble to final rule in 

section II.E, subsection “What is EPA’s Position on Certain Public Comments?” and response Essay 8.f.i 

for discussion on the differences between permit CS and WQS variances and when each is appropriate.

EPA believes that in some cases, both a WQS variance and a CS can provide the greatest water quality 

improvement in situations where the underlying designated use and criterion is not immediately 

attainable but the state or authorized tribe chooses to keep the underlying designated use as a longterm goal. See also response Essay 9.d for a discussion on why EPA did not include a provision to ensure 

that states and authorized tribes evaluate whether a permit CS can be used prior to pursuing a WQS 

variance.

B. When a Water Quality Standards Variance is Used to Undertake Studies to 

Determine the Attainability of Water Quality Standards or the Highest 

Attainable Condition, Those Studies Must be Properly Funded, Promptly 

Undertaken, Completed as Quickly as Possible, and Interim Best Management 

Practices Should Be Imposed as a Condition of Obtaining the Variance

EPA agrees with commenters that said any WQS variance that includes studies to determine the 

attainability of WQS or the HAC should ensure that those studies are performed as quickly as possible. 

However, EPA does not agree that requiring states and authorized tribes to fund specific activities or 

always requiring best management practices (BMPs) as a condition of a WQS variance is necessary.

The final rule includes several provisions to ensure that the requirements of a WQS variance are met as 

quickly as possible regardless of what those requirements may be. First, the final rule requires states 

and authorized tribes to provide to EPA documentation that the term of the WQS variance is only as 

long as necessary to achieve the HAC, and that such documentation must justify the term of the WQS 

variance by describing the activities and milestones that will occur during the WQS variance term (see 

section 131.14(b)(2)(ii)). In cases where a WQS variance requires the performance of certain studies, the 

state or authorized tribe must justify the term of the WQS variance in the context of the time required 

to perform those studies (as well as any other requirements of the WQS variance). Furthermore, the 

final rule specifies that any limitations and requirements necessary to implement the WQS variance shall 

be included as enforceable conditions of the implementing NPDES permit. Thus, any studies included as 

requirements of the WQS variance must be included as enforceable terms and conditions of the NPDES 

permit. EPA believes these provisions in the final rule will ensure that the requirements of a WQS 

variance, including studies of attainability, will be performed as quickly as possible. 

The final rule does not require the state or discharger(s) concerned to “properly fund and promptly 

undertake the necessary studies... to address the uncertainty of the appropriateness or attainability of 

the applicable water quality standards.” EPA determined it was not necessary to include such a 

requirement in the rule. If studies to address uncertainty are needed as part of any WQS variance, the 

terms of the WQS variance will determine the appropriate timelines for any such studies. The final rule 

does not limit states or authorized tribes from including such requirements in their regulations where it 

is consistent with state or tribal law.

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EPA agrees with commenters suggesting that the implementation of BMPs can be an important part of 

identifying and achieving the HAC for a WQS variance. Where a state or authorized tribe cannot identify 

any additional feasible pollutant control technology, the final rule provides the option of articulating the 

HAC as the greatest pollutant reduction achievable with optimization of currently installed pollutant 

control technologies and adoption and implementation of a pollutant minimization program (PMP). The 

final rule defines a PMP as a structured set of activities to improve processes and pollutant controls that 

will prevent and reduce pollutant loadings and thus is similar to BMPs. In this way a PMP is closely 

related or can lead to the implementation of BMPs. The rule makes this option available for a WQS 

variance that applies to a specific discharger(s) as well as a WQS variance applicable to a water body or 

waterbody segment. Pollutant control technologies represent a broad set of pollutant reduction 

options, including process or raw materials changes and pollution prevention technologies, practices 

that reduce pollutants prior to entering the wastewater treatment system, and BMPs for restoration and 

mitigation of the water body. This option requires states and authorized tribes to adopt the PMP along 

with other elements that comprise the HAC. As part of the applicable WQS, the permitting authority 

must use the PMP (along with the quantifiable expression of the “greatest pollutant reduction 

achievable”) to derive NPDES permit limits and requirements.

EPA disagrees with commenters who said the rule should explicitly require implementation of BMPs 

when a WQS variance involves studies of attainability. The final rule at section 131.14(b)(1)(ii) requires 

the interim requirements of any WQS variance to represent the HAC. If the implementation of one or 

more BMPs can result in higher ambient or effluent water quality, those BMPs would likely be included 

in the WQS variance to comply with the final rule. EPA explicitly requires a PMP in situations where a 

state or authorized tribe cannot identify any additional feasible pollutant control technology because it 

is especially important to ensure that states, authorized tribes, and dischargers consider all possible 

pollutant reductions, even when all feasible treatment technologies are already implemented. See 

response Essay 8.g.v for a discussion on BMPs and nonpoint sources (NPS) and EPA’s rationale for the 

final rule in relation to including or not including requirements for implementation of cost-effective and 

reasonable BMPs for NPS. 

C. Compliance Tools Must Provide a Path to Clean Water, Not an Exemption to 

Meeting Standards

EPA agrees with the commenters who said EPA should clarify that compliance tools such as WQS 

variances and permit CS should provide a path to clean water, not an exemption to meeting standards, 

and that EPA should provide more “direction” to states and authorized tribes on the appropriate use of 

WQS variances. EPA proposed and is finalizing section 131.14 in part because: “EPA has heard from 

states, tribes, and stakeholders that there is confusion, inconsistency, and mixed interpretations about 

how, when, and where variances may be used appropriately.” See 78 Fed. Reg. 54531 (September 4, 

2013). See section II.E of the preamble to the final rule for a full discussion of the requirements for WQS 

variances. In response to such comments, EPA has included extensive discussion in the preamble of the 

final rule about the appropriate use of WQS variances and permit CS. EPA also revised the proposed

section 131.14 to increase accountability and ensure states and authorized tribes utilize WQS variances 

to make progress toward designated uses. See response essay 8.b for discussion on how WQS variances 

function to make progress toward meeting underlying designated uses. See also response essay 8.f.i for 

a discussion on the provisions intended to increase accountability of WQS variances and on how the 

regulations limit WQS variances to serve as the time-limited applicable WQS for limited CWA purposes 

(i.e., development of NPDES permit limits and requirements and for use in 401 certification) while 

retaining the underlying use and criteria for other CWA purposes. See also response Essay 8.g.iii and 

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response Essay 8.g.iv, respectively, for more detailed discussions of the term of a WQS variance and the 

supporting documentation for WQS variances. See also response Essay 8.f for a discussion on EPA’s 

rationale for not including an explicit prohibition in the new WQS variance regulations on removal of 

existing uses.

D. Water Quality Standards Variances “Weaken” Water Quality Standards

The EPA disagrees with commenters who said WQS variances “weaken” standards or that WQS 

variances risk “leading the country to a point where not meeting water quality standards is the 

acceptable norm and variances the rule rather than its exception.” A commenter expressed concern that 

the WQS variance provisions would fail to provide the necessary assurances of CWA compliance and 

protection of treaty reserved resources. The WQS regulations allow states and authorized tribes to 

remove a designated use if the state or authorized tribe demonstrates the designated use is not 

attainable due to at least one of the six factors listed in section 131.10(g), even if the designated use is 

not attainable due to a single pollutant. The state or authorized tribe may feel pressure from the 

discharger to remove the designated use because the discharger would be unable to comply with the 

WQBEL for that pollutant. Instead of removing the designated use, however, a WQS variance can 

provide a regulatory mechanism to retain the designated use by providing time-limited relief to the 

discharger for the one pollutant that includes requirements to reduce pollutant loads to the waterbody.

A WQS variance is environmentally preferable to removing the designated use because the WQS 

variance is limited to a particular period of time, particular pollutants or pollutant parameters, and 

locations or dischargers. Moreover, a variance can provide a specific pathway to achieve feasible 

progress. In reviewing any state’s or authorized tribe’s adoption of a WQS variance, EPA will take into 

consideration any obligations regarding the need for protection of treaty reserved resources.

EPA’s regulation requires all NPDES permits to derive from and comply with all applicable WQS 

(section 122.44(d)). Because the final rule requires the state or authorized tribe to specify the HAC as 

the interim use and criteria, and the permitting authority must develop enforceable permit 

requirements that derive from and comply with the interim WQS of the WQS variance, the NPDES 

permit will include enforceable permit requirements that will lead to the highest water quality 

attainable. See the preamble to the final rule for more information about how WQS variances are 

implemented in NPDES permits. See response essay 8.b for discussion on how WQS variances function 

to make progress toward meeting underlying designated uses.

EPA recognizes commenter concerns that “the use of variances runs a very significant risk of leading the 

country to a point where not meeting water quality standards is the acceptable norm and variances the 

rule rather than its exception.” With this concern in mind, EPA revised the proposed final rule to include 

several provisions designed to ensure states and authorized tribes utilize WQS variances to make 

progress toward designated uses where there is uncertainty whether uses are ultimately attainable, and 

not to maintain the status quo of not meeting WQS. These provisions include a requirement that states 

and authorized tribes to justify the term of a WQS on the basis of the pollutant control activities to take 

place during the term of the WQS variance, reevaluate a WQS variance longer than five years at least 

every five years, submit the results of the reevaluations to the EPA within 30 days, include in the WQS 

variance a provision that the WQS variance will no longer apply if the state or authorized tribe does not 

perform the reevaluations on the specified schedule or does not submit the results to EPA within 30 

days, include a provision in the WQS variance providing that the requirements of the WQS variance are 

either the HAC identified at the time of the adoption of the WQS variance, or the HAC later identified 

during any reevaluation, whichever is more stringent, and include any limitations and requirements 

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necessary to implement the WQS variance as enforceable conditions of the NPDES permit for the 

permittee(s) subject to the WQS variance. EPA concludes that these and other provisions will ensure 

that WQS variance do not become “the acceptable norm.” 

E. EPA Should Better Explain the Difference between Water Quality Standards

Variances and Compliance Schedules

EPA revised the preamble in the proposed rule to better explain when using these WQS tools are 

appropriate. Sections E and F of the preamble to the final rule provides extensive discussion on the 

differences between a WQS variance and a CS, what each tool is designed to accomplish, and the 

appropriate circumstances states and authorized tribes may utilize them.

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Essay 8.f – Variances: Applicability

The U.S. Environmental Protection Agency (EPA) disagrees with the additions and deletions suggested 

by the commenter in reference to the proposed section 131.14(a) – Applicability. First, see response 

Essay 8.f.i for a discussion on EPA’s decision to retain applicability as proposed for single discharger, 

multiple discharger, and water quality standards (WQS) variances that apply to a water body or 

waterbody segment. In response to comments on regulatory text related to applicability of WQS 

variance for issuing Clean Water Act (CWA) section 401 certification, see response Essay 8.f.ii. In 

response to comments on the addition of language including a provision that addresses cost-effective 

and reasonable best management practices (BMPs) within the control of the permittee for single and 

multiple-discharger WQS variances, see response Essay 8.g.v. In regards to the comments related to 

compliance schedules (CS) and WQS variances, see response Essay 8.e.

In relation to the proposed provision section 131.14(a)(2)(i) that requires states and authorized tribes to 

retain the underlying designated use and criteria, the commenter requests deletion of language “unless 

the state adopts and EPA approves a revision to the underlying designated use and criterion consistent 

with § 131.10 or § 131.11.” EPA disagrees with this suggestion. EPA finds it necessary to include this 

language in the rule text related to WQS variances to ensure that where a state has an approved WQS 

variance and then has performed the proper analysis (i.e., use attainability analysis [UAA] or a “use and 

value demonstration”) and submitted a use change and EPA approves such a change, that the 

regulations are clear as to which designated use and criteria apply. This is consistent with CWA section 

101(a) which recognizes that not all uses are attainable. This language does not authorize any revisions 

to designated uses and water quality criteria beyond those that would otherwise already be allowed 

under the regulations at section 131.10 that govern the adoption and revision of designated uses and 

section 131.11 which govern the adoption and revision of water quality criteria to protect such uses. 

In response to the comment that EPA should add a provision to section 131.14 to protect existing uses

because that is an “absolute floor” of water quality, EPA agrees that existing uses are an “absolute 

floor.” However, EPA disagrees that such an approach is necessary to protect existing uses. Unlike a 

designated use change which changes the ultimate desired condition for a water body, the purpose of a 

WQS variance is to provide a mechanism that will facilitate incremental progress toward achieving the 

currently adopted designated use (and thus the existing use, if one is not being attained) in an 

accountable and transparent manner. Such a tool would be unavailable to states and authorized tribes if 

EPA included a provision that prohibits WQS variances where the time-limited “designated use and 

criterion remove necessary protections for existing uses” (as suggested by the commenter). On the 

other hand, allowing the use of a WQS variance independent of the existing use would promote the 

environmental outcome to “restore” water quality consistent with the CWA objective to restore and 

maintain the chemical, physical, and biological integrity of the Nation’s waters. However, EPA agrees 

that it is imperative that WQS variances do not make the water quality worse than what it currently is 

and has thus specifically included a provision in section 131.14(b)(1)(ii) to ensure that WQS variances do 

not result in any lowering of the currently attained ambient water quality which would jeopardize 

meeting the CWA objective. This provision includes a single exception for the situation where a WQS 

variance is necessary for restoration activities under section 131.14(b)(2)(i)(A)(2)). The provision at 

section 131.14(b)(1)(ii) is consistent with the purpose of a WQS variance to facilitate the restoration of 

water quality rather than serving as a mechanism to lock in status quo.

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Essay 8.f.i – Variances Applicability: Scope

A. Water Quality Standards Variances Are Water Quality Standards

The U.S. Environmental Protection Agency (EPA) thanks and agrees with commenters who generally 

support water quality standards (WQS) variances as an appropriate WQS tool. See section II.E of the 

preamble to the final rule for a thorough discussion of WQS variances.

EPA does not agree with comments suggesting WQS variances are not WQS subject to EPA review and 

approval. WQS variances are WQS that EPA has the authority and duty to review under Clean Water Act 

(CWA) section 303(c). As described in EPA’s “What is a New or Revised Water Quality Standard Under 

CWA 303(c)(3)?” (http://water.epa.gov/scitech/swguidance/standards/cwa303faq.cfm; October 2012, 

EPA Document #820-F-12-017), based on the requirements under the CWA at 303(c)(3), EPA’s 

regulations and case law. EPA identified the following four key factors in identifying what is a WQS:

1. It is a legally binding provision adopted or established pursuant to state or tribal law;

2. The provision addresses designated uses, water quality criteria (narrative or numeric) to 

protect designated uses, and/or antidegradation requirements for waters of the United States;

3. The provision expresses or establishes the desired condition (e.g., uses, criteria) or instream level 

of protection (e.g., antidegradation requirements) for waters of the United States immediately or 

mandates how it will be expressed or established for such waters in the future; and

4. The provision establishes a new WQS or revises an existing WQS. 

Because a WQS variance is defined as a time-limited designated use and criterion, and because 

variances effectively establish the desired condition of waters of the U.S. over that defined limited time, 

any new or revised WQS variance that has been duly adopted pursuant to state law would meet each of 

the four factors described above. As a new or revised WQS, EPA has the authority and duty to review 

and approve or disapprove variances.

EPA does not agree with several commenters’ suggestions that EPA only needs to approve WQS 

variance policies or procedures and that the WQS variances, as applied, do not need EPA approval. As 

discussed above, a WQS variance is a new or revised WQS. As such, it does not become an applicable 

WQS for CWA purposes (in the case of WQS variances, those purposes are for National Pollutant 

Discharge Elimination System (NPDES) permitting and 401 certifications) unless and until EPA has 

approved the new or revised WQS. EPA approval of a WQS variance as a WQS is essential for NPDES 

permits that implement a WQS variance. The permit regulations at section 122.44(d)(1)(vii)(A) require 

permits to derive from and comply with applicable WQS. If there is no approved WQS variance effective 

for CWA purposes upon which to base the NPDES permit limits and requirements, then the permit 

would have to be written to the underlying WQS or it could be subject to objection and challenge. EPA 

review of only policies and procedures authorizing states and tribes to adopt WQS variances, even 

legally binding policies and procedures authorizing WQS variances, would not alone be sufficient to 

make the WQS variances issued by the states and authorized tribes the applicable WQS for NPDES and 

401 purposes. Additionally, EPA’s review of authorizing policies alone would not include sufficient 

information (e.g., the economic particulars of a facility seeking a WQS variance under the substantial 

and widespread economic and social impact justification) for EPA to determine whether or not the WQS 

variance, as applied, would satisfy federal requirements. EPA’s review and approval of individual WQS 

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variances is also important because EPA must evaluate whether WQS variances in particular 

circumstances (whether for individual or multiple dischargers) satisfy the requirements set forth in this 

rulemaking for establishing alternate time-limited WQS. 

EPA also does not agree with the comment that points to the “General Policies” chapter of EPA’s WQS 

Handbook as a rationale for why only WQS variance policies (and not WQS variances themselves) are 

WQS subject to EPA review and approval or disapproval. EPA acknowledges that its 1983 regulations 

provided that if states adopted general implementation policies in the WQS, they would be subject to 

EPA approval. However, it has been EPA’s longstanding position that EPA also must approve individual 

WQS variances (see also EPA’s response to code 8.b – Variance: General Opposition). The 1977 OGC 

memorandum that opined states could adopt variances as an alternative to a permanent downgrade of

a use was issued in the context of a state adopting and EPA approving a revised WQS. As discussed 

above, EPA considers WQS variances to be WQS. EPA does not view its position that WQS variances are 

WQS as a change in Agency interpretation. To the extent the commenter is asserting that EPA has 

changed its interpretation, the final rule at 131.14 represents the Agency’s interpretation issued 

following notice and comment rulemaking. EPA notes that in 2014, it updated certain chapters of the 

online version of the Handbook to ensure it reflected previously publicly articulated guidance. EPA also 

does not agree with the commenter’s contention that the Star-Kist decision precludes EPA from taking 

action on regulations regarding “whether and how variances are used,” since such action would fall in 

the realm of implementation of standards. For further discussion regarding WQS variance 

implementation please see Response Essay 8.h.

EPA notes that states and authorized tribes may take advantage of the public process that they currently 

use for NPDES permit issuance for obtaining public input on a proposed WQS variance when that public 

process is consistent with EPA’s regulations at section 131.20(b), including the requirements related to 

holding a public hearing. Once the WQS variance is adopted, they can submit the WQS variance to EPA 

for review under CWA section 303(c). See section II.E of the preamble to the final rule for more 

information on ways states and authorized tribes can streamline the process for WQS variance adoption.

B. Water Quality Standards Variances, Compliance Schedules, and Mixing Zones

Some commenters expressed confusion or requested clarity regarding the differences between WQS 

variances, compliance schedules (CS), and mixing zones. A critical distinction between the three is that 

individual WQS variances are themselves WQS, establishing the desired condition of water quality and 

serving as the applicable WQS for NPDES permitting. As described in subsection A of this essay, an 

important feature of a WQS variance is that it is a WQS and, therefore, for the purposes of NPDES 

permitting under CWA section 402, it can be used as the basis for deriving permit limits and 

requirements that comply with the applicable WQS per section 122.44(d)(1)(vii)(A). In contrast, 

individual CS and individual mixing zones are not WQS. They do not establish the desired condition of 

water quality or serve as the WQS on which NPDES permit limits and requirements are derived.

Individual CS provide time for a discharger to come into compliance with its NPDES permit limits and 

requirements derived from the applicable WQS. Mixing zones can be allowed as long as the permit limits 

and requirements will ensure the applicable WQS are met in the waterbody as a whole. States and 

authorized tribes do need to authorize the use of mixing zones and CS in deriving permit limits and 

requirements, but because neither individual CS nor individual mixing zones change WQS, neither needs 

EPA approval. See section II.F of the preamble to the final rule for more information on compliance 

schedule authorizing provisions (CSAPs). See also Response Essay 9.b for additional discussion on the 

distinction between CSAPs and CS themselves.

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EPA does not agree with commenters who suggested that “variances aren’t really necessary – mixing 

zones do the same thing.” As noted above, the two tools serve different functions and have different 

modes of operation with regard to the designated use and criteria of the water body. WQS variances are 

defined in the final rule as “a time-limited designated use and criterion for a specific pollutant(s) or 

water quality parameter(s) that reflect the highest attainable condition (HAC) during the term of the 

WQS variance.” As described in EPA’s WQS Handbook1

, 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. An important concept in the use of mixing zones is that 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. When states or authorized tribes grant a WQS variance, they are, in effect, allowing a 

different designated use and criteria to serve as the applicable WQS for the limited purposes of CWA 

section 402 permitting and issuing CWA section 401 certifications. On the contrary, when states or 

authorized tribes establish a mixing zone in the development of a particular NPDES discharge permit, the 

mixing zone allows an exceedance of the applicable criteria in that defined location while maintaining 

the designated use and criteria of the waterbody as a whole. See the WQS Handbook, Chapter 5 for 

more information on mixing zones.

C. Water Quality Standards Variances for Water Bodies or Waterbody 

Segments

EPA notes that numerous commenters supported WQS variances being applicable to a specific 

discharger, multiple dischargers, or a water body or waterbody segment. The final rule retains this 

applicability. EPA carefully considered comments suggesting that EPA should eliminate the option for a 

WQS variance to apply to a water body or waterbody segment (hereafter referred to as a “waterbody 

variance”) but does not agree with those comments. The purpose of a waterbody variance is to provide 

an alternative to removing or downgrading the designated use of a waterbody and instead make 

incremental improvements in water quality while retaining the long term goal of fully attaining the 

designated use. A waterbody variance serves the national goal in section 101(a)(2) of the Act and the 

ultimate objective of the CWA to restore and maintain the chemical, physical, and biological integrity of 

the Nation’s waters because the WQS variance is narrow in scope (with regard to the subject pollutants)

and duration and are designed to make progress toward water quality goals. 

Where a state or authorized tribe can demonstrate that a designated use and criterion currently in place 

for a specific pollutant(s) is not attainable for a limited period of time for an entire water body or 

waterbody segment, the state or authorized tribe may adopt a waterbody variance. In such 

circumstances, the WQS variance would apply to the water body itself, rather than to any specific source 

or sources, much like a use change. However, unlike a use change, the WQS variance is tailored narrowly

to the specific pollutant(s) for a particular limited time-frame, and is only applicable for CWA section 402 

purposes or for issuing certifications under CWA section 401, while the underlying WQS remains in place 

for those CWA purposes that relate to the long term goal of the waterbody (e.g., CWA section 303(d)). A 

waterbody variance provides time for the state or authorized tribe to work with both point and 

nonpoint sources (NPS) to determine and implement adaptive management approaches on a 

waterbody/ watershed scale that will achieve reductions in the pollutant(s) specified in the waterbody 

variance, and to make progress toward fully attaining the designated use (78 FR 54532). 

 

1 EPA Water Quality Standards Handbook, http://water.epa.gov/scitech/swguidance/standards/handbook/

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Based on comments, EPA refined the regulatory structure of the final rule to better promote progress by 

including provisions for WQS variances that maximize accountability while minimizing rulemaking 

burden for all WQS variances. See section II.E of the preamble to the final rule for more discussion on 

the regulatory structure of section 131.14.

EPA agrees with the comment that a particular state or authorized tribe may not find the concept of 

waterbody variances useful or may not be ready to use this tool. States and authorized tribes do not 

need to utilize WQS variances (waterbody variances or other) as they are a discretionary aspect of the 

WQS program. However, many states have expressed support and desire for such a tool now. An 

interested state or authorized tribe may use their discretion to pursue a waterbody variance wherever a 

WQS variance may be appropriate to deal with more significant or widespread pollution problems, such 

as where NPS are a major source of pollutant loadings. A waterbody variance could be particularly 

successful where the state or authorized tribe finds that both point and NPS are willing to collaborate on 

a strategy to resolve the pollution challenges in the waterbody. If a total maximum daily load (TMDL) 

has been developed, a state or authorized tribe could choose to utilize a waterbody variance as a 

regulatory framework within which to establish a TMDL implementation plan specifying requirements, 

actions and/or milestones for which both point and NPS are accountable to achieve the waste load and 

load allocations of the TMDL and interim targets for the water body. A waterbody variance could also be 

useful in situations where the state or authorized tribe does not know whether the designated use and 

criterion can be attained, but feasible progress toward attaining the designated use and criterion can 

still be made by implementing known controls and tracking environmental improvements. For example, 

a state or authorized tribe could adopt a waterbody variance for a persistent organic pollutant in a 

situation where all dischargers to the waterbody are already implementing pollutant control 

technologies with the greatest pollutant reduction that is feasible. In such a case, section 

131.14(b)(1)(ii)(B)(2) provides for the option of adopting a waterbody variance that requires the 

permittees to maintain their current pollutant control technology and implement a pollutant 

minimization program (PMP) while the state addresses NPS of the pollutant.

In situations where a state or authorized tribe uses a waterbody variance to address point and NPS, EPA 

also recognizes the need for additional accountability. In addition to the provisions that EPA added to 

the final rule that apply to all WQS variances to maximize accountability and to achieve progress 

towards the underlying designated use and criteria, the final rule includes several provisions to ensure

that a state or tribe consider all sources of the specified pollutant(s) when developing a waterbody 

variance with input from their public. For example, under the final regulations at section

131.14(b)(1)(ii)(B), EPA has made it clear that the articulation of the HAC for a waterbody variance is 

different than the articulation for discharger(s)-specific WQS variances because a waterbody variance

expresses the desired condition of the entire water body or waterbody segment for the particular 

pollutant(s) and time period (for limited CWA purposes) and therefore, EPA does not allow the flexibility 

to express the HAC as an effluent condition. Where a state or authorized tribe chooses to submit a 

waterbody variance for EPA approval, EPA expects the submission to include the identified HAC during 

the term of the WQS variance to take into account feasible reductions and pollutant minimization 

actions. These additional provisions plus the provisions discussed below to increase transparency and 

consideration of NPS, address concerns by some commenters who criticized waterbody variances for 

not having rigorous enough requirements for the granting of such variances and sufficient assurances 

for progress during the term of the variance. EPA carefully considered these comments and developed 

its final regulations with these comments in mind, intending to ensure that waterbody variances would 

only be used in appropriate situations and would result in the highest water quality attainable during 

the term of the variance.

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EPA also included provisions intended to increase transparency and consideration of multiple sources of 

the pollutant(s), including NPS, as they can have a significant influence on whether the designated use 

and associated criteria for the entire water body are attainable. Specifically, EPA is requiring 

identification and documentation of any cost-effective and reasonable best management practices 

(BMPs) for NPS controls related to the pollutant(s) or water quality parameter(s) and water body or 

waterbody segment(s) specified in the waterbody variance that could be implemented to make progress 

towards attaining the underlying designated use and criterion. This includes a requirement that states 

and authorized tribes provide public notice and comment for any such documentation. Also, any 

subsequent WQS variance for a water body or waterbody segment must include documentation of 

whether and to what extent BMPs were implemented to address the pollutant(s) or water quality 

parameter(s) subject to the waterbody variance and the water quality progress achieved. Because 

waterbody variances relate to the entire water body or waterbody segment and will likely require the 

cooperation of both point- and NPS of the pollutant(s), these requirements may help identify potential 

actions that facilitate meeting the HAC specified in the waterbody variance. In addition, requiring states 

and authorized tribes to provide the public with information about the potential impact of controlling 

NPS of pollutants increases public transparency and will help inform the re-evaluation process (required 

in the final rule for any WQS variances greater than five years). See also Response Essay 8.g.v for 

discussion on the requirement related to BMPs for NPS for waterbody variances.

D. Water Quality Standards Variances and “Narrowed” Clean Water Act 

Purposes

In response to comments on limiting the use of WQS variances to CWA section 402 (NPDES permitting) 

and when issuing certifications under section 401 of the Act, and not applying variances for TMDL 

development under CWA sections 303(d) and 305(b), see EPA’s response to code 8.f.ii – Variances 

Applicability: Approved Variances and Permitting and 303(d).

EPA does not agree with the commenter who states that EPA’s proposed provision to ensure that states 

and authorized tribes retain the underlying standard in their WQS while still allowing the WQS variance 

to apply for limited CWA purposes is in conflict with the requirements of CWA section 303(c)(3). The 

commenter argues that section 131.21(d) “precludes EPA from utilizing a bifurcated approach for 

implementing WQS by allowing the most recently adopted and approved WQS for a water body (or 

portion of a water body) to be used for one purpose of the Act and a previously adopted and approved 

...WQS for the same waters... to be used for another use of the Act.” EPA does not agree with this 

commenter’s limiting interpretation of the Act and regulation, and believes the Agency has the authority 

to apply variances for limited CWA purposes as has been its longstanding practice to do so. That said,

the final regulations include section 131.14(a)(3) to make clear that when an approved WQS variance is 

in place, the applicable standard under sections 131.21(d)-(e) is the WQS variance for developing NPDES 

permit limits and requirements under 301(b)(1)(C) and for when states or other certifying entities issue

certifications under CWA section 401. This addition of section 131.14(a)(3) modifies the interpretation of 

“applicable standard” for applying sections 131.21(d)-(e) and CWA section 303(c)(3) for WQS variances. 

To the extent that this is a change in regulatory interpretation, EPA may do so through notice and 

comment rulemaking as the Agency has done in this rulemaking.

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E. Addressing the Need for More Accountability and Flexibility for Water 

Quality Standards Variances

As described in detail in section II.E of the preamble to the final rule, based on comments, EPA revised 

some aspects of section 131.14 to maximize accountability related to adopting and implementing WQS 

variances while minimizing burden related to state or tribal rulemakings for adopting WQS variances. In 

addition to requiring that each WQS variance specify the term of the variance (i.e., expiration date), EPA 

also included several other provisions. Specifically, for any WQS variance that is greater than five years, 

EPA included provisions at section 131.14(b)(1)(iii), (v), and (vi) that ensure timely reevaluation of the 

WQS variance and ensure that states and authorized tribes acquire and use updated information on the 

HAC to inform the NPDES permitting process. EPA also clarified the regulatory text pertaining the 

documentation supporting the term of the WQS variance (see section 131.14(b)(2)(ii)) so that states and 

authorized tribes must describe the pollutant control activities to achieve the HAC which will then serve 

as milestones for the WQS variances. Such activities/milestones may be used by the permitting authority 

in developing permit limits and requirements. Finally, EPA’s regulation at section 131.14(c) makes it 

clear that states and authorized tribes must include any limitation and requirement necessary to 

implement the WQS variance as enforceable conditions of the NPDES permit for the permittee(s) 

subject to the WQS variance. See also Response Essay 8.g.iii for additional discussion on the 

reevaluation related provisions.

In regards to comments about the public identification of all dischargers in the WQS variance, both the 

proposed rule and final rule include a provision requiring the state or authorized tribe to identify the 

discharger(s) in the WQS variance. A State or authorized tribe may satisfy the requirements at section

131.14(b)(1)(i) for multiple discharger WQS variances by including a list of (1) the pollutant(s) or water 

quality parameter(s), (2) the name/location of the water body/waterbody segment(s) and (3) the name 

of the dischargers subject to the WQS variance. As an alternative, a state or authorized tribe may satisfy 

section 131.14(b)(1)(i) by including (1) a list of the pollutant(s) or water quality parameter(s), (2) a 

description of the specific characteristics of any discharge and discharger subject to the WQS variance, 

(3) an identification of the underlying designated use and water quality criteria of the respective 

receiving water bodies/waterbody segments addressed in the WQS variance as a proxy for 

name/location, and (4) information where the public can access the website or document that the state 

or authorized tribe will subsequently update with the names of the dischargers covered by the WQS 

variance as the WQS variance is implemented in specific discharger permits. EPA expects that the same 

characteristics used to group the dischargers will be used to identify dischargers when using the second

approach. As discussed in EPA’s Frequently Asked Questions (FAQs), EPA advised that in justifying the 

need for a multiple-discharger WQS variance, the state’s demonstration should “Group permittees 

based on specific characteristics or technical and economic scenarios that the permittees share (e.g., 

type of discharger (public or private), industrial classification, permittee size and/or effluent quality, 

treatment train (existing or needed), pollutant treatability, available revenue, whether or not the 

permittee can achieve a level of effluent quality comparable to the other permittees in the group, 

and/or waterbody or watershed characteristics)” (EPA-820-F-13-012, March 2013). This approach will 

allow a state or authorized tribe to adopt the WQS multiple discharger variance for those dischargers 

that currently qualify and then, as additional qualifying dischargers’ permits come up for renewal, those 

dischargers (already approved because they meet the description/selection characteristics) can be 

subject to the WQS variance.

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In the preamble to the final rule (see section II. E, “What is EPA’s position on certain public 

comments?”), EPA also discusses possible ways for states and authorized tribes to streamline the 

administrative processes of adopting WQS variances. One commenter suggests that EPA allow states 

and authorized tribes to use the “performance-based approach” for streamlining submittal and review 

of WQS variances. See response 8.g.iii subheading K for EPA’s explanation regarding why it does not 

agree with this suggestion.

EPA does not agree with the comment that “the main problem with U.S. EPA’s variance process is that it 

must meet the same requirements as a permanent designated use modification.” EPA addressed this 

issue in the preamble to the proposed rule when the Agency explained it’s rationale for including an 

entirely new, separate section for WQS variances in the rulemaking (see 78 FR 54531-32).

See also response 8.b for discussion of why EPA views WQS variances as a necessary and appropriate 

tool. See also response 8.d for further discussion of why and how EPA views WQS variances as 

practicable. See also response 8.f for additional discussion on WQS variances and the protection of 

existing uses and current water quality.

F. Other

New Dischargers

EPA does not agree with the commenter who requested that EPA prohibit WQS variances for “new 

dischargers.” Specifically, the term “new discharger” is defined in the NPDES permitting regulations at 

section 122.22 and has a very particular meaning that is not the same as the laymen’s meaning. Section

122.2 defines a “new discharger” in relation to the date EPA published the relevant industry effluent 

guidelines (i.e., technology-based regulations). The goal of a prohibition on WQS variances for a facility 

that is recently built and commences discharge would be to ensure that such facilities plan to

incorporate the best pollutant reduction technology to meet all applicable WQS(as well as their 

technology-based limitations) before they commence discharge. EPA concluded it would be confusing to 

prohibit WQS variances for “new dischargers” if that discharger began discharging decades ago (but 

after the relevant technology-based effluent guidelines regulation so that it meets the definition of 

“new discharger”) and is then faced with a new or more stringent WQS (and resulting water qualitybased effluent limit [WQBEL]). This is especially of concern where the discharge has been in place and a

new/revised WQS criteria value is below the achievable treatment level of existing technology. A WQS 

variance is a tool that can be used to provide time until new technology exists while the discharger 

implements pollutant minimization practices to make environmental progress. A prohibition on “new 

dischargers” would present an artificial barrier to that progress. Additionally, EPA addressed the 

fundamental principal that WQS variances must not result in any lowering of the currently attained 

ambient water quality through the provision in the final rule at section 131.14(b)(1)(ii) (see also 

Response Essay 8.f for more detail regarding EPA’s thinking on this provision).

 

2 New discharger means any building, structure, facility, or installation: (a) From which there is or may be a 

‘‘discharge of pollutants;’’ (b) That did not commence the ‘‘discharge of pollutants’’ at a particular ‘‘site’’ prior to 

August 13, 1979; (c) Which is not a ‘‘new source;’’ and (d) Which has never received a finally effective NDPES 

permit for discharges at that ‘‘site.’’

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Permit Waivers

One commenter suggests that EPA’s WQS variance regulations at 131.14 removes the state’s flexibility 

“to grant waivers due to extreme events (such as temporary relief during droughts and natural 

disasters).” The final rule does not address temporary waivers of the nature described by the 

commenter, and the commenter does not explain the conditions under which the final rule removes 

state flexibility.

See Response Essay 3.a for discussion on concerns regarding state primacy and Response Essay 8.m 

regarding EPA’s legal authority for WQS variances and the requirements in the final rule. See Response 

Essay 8.i for discussion on WQS variance renewals. See Response Essay 8.c for responses concerning 

changes to the definition of WQS variance. See Response Essay 12.c for a discussion on EPA’s estimates 

of burden and costs for the rule.

Regarding comments pertaining to section 131.14(a)(2)(i), see Response Essay 8.f for discussion on why 

EPA has retained the provision.

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Essay 8.f.ii – Variances Applicability: Approved Variances and Permitting 

and 303(d)

A. Water Quality Standards Variances and Clean Water Act Purposes

The U.S. Environmental Protection Agency (EPA) appreciates comments that support limiting the use of 

water quality standards (WQS) variances to permits issued under Clean Water Act (CWA) section 402 

(National Pollutant Discharge Elimination System [NPDES]) and to certifications issued under section 401 

of the Act. EPA appreciates comments that support EPA’s provision at section 131.14(a)(2) which 

clarifies that “all other applicable standards not specifically addressed by the WQS variance remain 

applicable.” Keeping the applicability of WQS variances to a specific pollutant(s) along with limited CWA 

purposes, limited timeframe, and reevaluation for longer term variances while retaining the underlying 

standards are important components to the WQS variance framework in the final rule.

In response to comments on the need for increased flexibility and accountability for WQS variances, see 

section II.E of the preamble to the final rule which includes a discussion on the revisions EPA made to 

the final rule to increase the accountability, flexibility, and transparency of WQS variances.

EPA disagrees with commenters who suggest that a state or authorized tribe should use the WQS 

variance as the basis for waterbody assessment and listing or for total maximum daily load (TMDL) 

development under CWA sections 303(d) and 305(b). EPA carefully evaluated this issue and as discussed 

in the proposed rule preamble and in the final rule preamble in section II.E, EPA concluded that in order 

to make incremental water quality improvements it is important that states’ and authorized tribes’ WQS 

continue to reflect the ultimate water quality goal unless the state or authorized tribe adopts a 

permanent use downgrade that is approved by EPA. Therefore, the final rule requires states and 

authorized tribes to retain the underlying designated use and criterion in their standards to apply to all 

other permittees not addressed in the WQS variance. States and authorized tribes must also retain the 

underlying designated use and criterion for identifying threatened and impaired waters under CWA 

section 303(d), and for establishing TMDLs.1 EPA emphasizes that this is appropriate for WQS variances 

that apply to a single discharger or multiple dischargers, and to WQS variances that apply to a water 

body or to a waterbody segment. This is especially important for CWA section 303(d) listings, in 

particular when a variance is for individual dischargers. If the water is not attaining the underlying use 

and criteria which continue to be applicable WQS for CWA purposes, these waters must be identified as 

impaired consisted with CWA section 303(d)(1)(A). It is important that the public understand the waters 

remain in nonattainment. EPA disagrees with the comment that “where a variance is applicable to 

certain discharges, any 303(d) listings should be deferred...since a TMDL is not necessary to address a 

short-term variance...” Based on EPA’s position, as described above, CWA section 303(d) listings and 

TMDL development need to continue to be based on the underlying standard. However, EPA does allow 

prioritization of TMDL development. For example, it may be possible for a state to place a waterbody 

with a WQS variance on a lower priority for TMDL development until after the variance has expired. A 

comment expressed concern that if a WQS variance cannot be used for identifying impaired waters 

under CWA section 303(d), and, therefore, the underlying standard is used as a basis for 303(d) listing, 

then new or expanded discharges under section 122.44 will be prohibited. Decisions regarding issuance 

 

1 See 78 Fed. Reg. 54533 (September 4, 2013).

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of permits for expanded discharges to impaired waters are made case-by-case consistent with the 

applicable NPDES rules. As described in subsection D of this essay, the final rule provisions at section

131.14 do not prohibit issuance of permits for new or expanded discharges. The final rule does require 

that a WQS variance may not allow the lowering of “currently attained water quality.” See response 

Essay 8.f.i for additional discussion of WQS variances and CWA purposes in regards to sections

131.21(c)-(e).

EPA has also clarified language in the final rule at section 131.14(a)(3) in response to comments 

requesting better articulation of the applicability of WQS variances. See section II.E and the final 

regulatory text for a discussion of EPA’s rationale.

B. Permits, Total Maximum Daily Loads, and Water Quality Standards

Variances

As described in section II.E of the preamble to the final rule, EPA received comments questioning how a 

WQS variance works with a TMDL and CWA section 303(d) impaired waters listing(s). These comments 

suggested the proposed rule would create a conflict in how the NPDES permitting regulation requires 

permitting authorities to develop water quality-based effluent limits (WQBELs). Section 

122.44(d)(1)(vii)(A) specifies that all WQBELs in an NPDES permit must derive from and comply with all 

applicable WQS. Section 122.44(d)(1)(vii)(B) specifies that the WQBEL of any NPDES permit must be 

consistent with the assumptions and requirements of any available (emphasis added) wasteload 

allocation (WLA) in an EPA-approved or EPA-established TMDL. Because the WLA of the TMDL would 

need to be based on the underlying designated use and criterion (and not on the highest attainable 

condition (HAC) established in the WQS variance), then the WLA in the TMDL is not available (or 

applicable) to the permittee covered by the WQS variance for NPDES permitting purposes while the 

WQS variance is in effect. The permitting authority would need to develop WQBELs for the permittees 

subject to the WQS variance based on the interim requirements specified in the WQS variance. Upon 

termination of the WQS variance, the NPDES permit would need to again derive from and comply with 

the underlying designated use and criterion and be consistent with the assumptions and requirements 

of the WLA (as it is again “available”).

In a related comment, one commenter requested that EPA clarify in rule and preamble that the WQS 

applicable to the discharger should be considered to be the variance, not the underlying standards and 

provided specific suggested edits to the regulatory text. EPA agrees in concept with this commenter and 

has reflected that understanding in the final rule at section 131.14(a)(3) and section 131.14(c) and in 

section II.E of the preamble to the final rule. However, EPA chose to meet that objective through 

selection of different revised regulatory text. For example, the commenter suggested EPA add that the 

variance “... supercedes any wasteload allocation during the variance period.” Such language is 

unnecessary because EPA achieved the same goal by revising the final rule at section 131.14(a)(3) to

1) clarify the application to developing permit limits, and 2) to include a direct reference to 122.44(d) at 

section 131.14(c). Another commenter requested that EPA clarify that a WQS variance can be the 

“applicable” WQS for the purposes of section 122.4(i) related to new dischargers. The final rule is clear 

that an EPA approved WQS variance is the applicable standard for developing NPDES permit limitations 

and requirements (see section 131.14(a)(3)). EPA also notes, however, that the WQS variance for a new 

discharger must also comply with the final regulation at section 131.14(b)(1)(ii), which specifically 

prohibits a WQS variance that would allow the lowering of “currently attained water quality”(with the 

single exception related to the WQS variances based on the new factor for dam removal or wetland, 

lake, or stream restoration). EPA reminds the commenter that new dischargers have an opportunity to 

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put the latest technologies and pollution minimization strategies in place. See also discussion in EPA’s 

response to code 8.f.i – Variances Applicability: Scope.

C. Water Quality Standards Variance and Permit Term Expiration

Commenters raised questions about what happens when the WQS variance expiration and the permit 

expiration are not well coordinated. NPDES permits are issued on a standard 5-year cycle, while 

variances can be adopted and approved for a variety of different time periods. Commenters also said 

EPA should clarify that interim permit limits and other variance conditions continue to apply until such 

time as a variance or permit is renewed. Commenters questioned if a “variance must be as short as 

possible...” means that EPA could require WQS variances to last less than one permit term, and 

suggested that such a requirement “could cause issues with the permit backlog by creating the need to 

modify and reissue permits mid-term.” First, the final rule specifies that the term of a WQS variance 

must be only as long as necessary to achieve the HAC. Second, EPA recommends that permitting 

authorities and state and authorized tribes work to coordinate permit issuance/renewal with the 

duration of the related WQS variance. In addition, where a state or authorized tribe is adopting a WQS 

variance that is longer than 5 years, the final rule requires that the state or authorized tribe must

identify a schedule (no longer than 5 years) for reevaluation of the WQS variance. EPA understands that 

states and authorized tribes are likely to time the reevaluation with either the triennial review or the 

permit cycle so that information can be timely for permit renewal. However, in the situation where a 

state or authorized tribe does not coordinate a WQS variance term with the expiration date of an NPDES 

permit, and the information is available to the permitting authority indicating that the term of a WQS 

variance will end during the permit cycle, the permitting authority would need to develop two WQBELs: 

one WQBEL based on the HAC applicable throughout the WQS variance term, and another WQBEL 

based on the underlying designated use and criterion to apply after the WQS variance terminates (see 

discussion in section II.E of the preamble to final rule). Including two sets of WQBELs that apply at 

different time periods in the permit ensures that the permit will derive from and comply with WQS 

throughout the permit cycle. If the state or authorized tribe adopts and EPA approves a subsequent 

WQS variance during the permit term to replace an expiring WQS variance, the new WQS variance 

would constitute “new regulations” pursuant to section 122.62(a)(3)(i), and the permitting authority 

could modify the permit to derive from and comply with the subsequent WQS variance. At the request 

of the permittee, the permitting authority can also utilize the “Permit Actions” condition in a permit

required by section 122.41(f) to modify a permit pursuant to section 122.62 and revise the WQBEL to 

reflect the new WQS variance.

On the other hand, there might be a situation where the state or authorized tribe adopts, and EPA 

approves, a WQS variance with a specific duration (as required by section 131.14(b)(1)(iv)) that is set to 

match the 5 year permit cycle or is longer than one permit cycle and, subsequently, the permit expires 

and is administratively continued (as may be authorized under state or Federal regulations). 

Importantly, because the final rule requires that states and authorized tribes specify the requirements 

that apply throughout the term of the WQS variance and that those requirements represent the HAC of 

the water body or waterbody segment applicable throughout the term of the WQS variance (section

131.14(b)(1)(ii)), the WQBELs and the permit terms and conditions in the administratively continued 

permit will reflect the highest attainable use (HAU) and will continue to derive from and comply with the 

WQS variance. If the administratively continued permit is in effect when the WQS variance expires, the 

WQBELs in the permit remain the applicable requirement. EPA encourages permitting authorities to 

prioritize renewal of those permits that they developed based on a WQS variance that has expired or 

where the reevaluations have identified a higher attainable condition. EPA notes that the final 

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regulations require that WQS variances longer than five years include a statement providing that the 

requirements of the WQS variance are either the HAC identified at the time of the adoption of the WQS 

variance, or the HAC later identified during any reevaluation, whichever is more stringent. This enables 

permit renewal based on an updated HAC without separate state or authorized tribal adoption and EPA 

approval of more stringent interim requirements in the WQS variance. 

D. Clean Water Act Section 401 Certification, Variances, and Compliance 

Schedules

EPA disagrees with commenters who articulated that EPA needed to revise the regulation to clarify that 

WQS variances are discretionary. The final rule language in 131.14 clearly specifies: “States may adopt 

WQS variances...” In the context of the regulation, EPA uses the word “may” (as opposed to “must” or 

“shall”) when a requirement is optional. A state’s or authorized tribe’s use of WQS variances or their 

inclusion of a compliance schedule authorizing provision (CSAP) in their WQS is discretionary. (See EPA’s 

response to code 9.b regarding the need for a CSAP when including compliance schedules (CS) in NPDES 

permits.) For additional discussion on CSAPs, see section II.F of the preamble to the final rule.

EPA also disagrees with commenters that requested EPA to revise the final rule to make clear that a 

“variance is not required whenever a schedule of compliance is needed because the permitted facility is 

not currently in compliance and it is infeasible to bring the facility into immediate compliance.” WQS 

variances are discretionary tools and, as discussed in section II.E of the preamble to the final rule, they 

are intended to serve a different purpose from CS. However, also as discussed in section II.E of the 

preamble to the final rule, under the final rule it is conceivable that a state or authorized tribe may 

utilize both tools in coordination to give a permittee relief from the underlying WQS and time to achieve 

the HAC by the end of the duration of the WQS variance. See also EPA’s response to code 8.e – 

Variances: Variances vs. Compliance Schedules for a discussion on the use of WQS variances and CS. 

Based on comments, EPA revised the regulatory text to better describe how states and authorized tribes 

can use WQS variances in the context of CWA section 401 certification (see section 131.14(a)(3) and

section II.E of the preamble to the final rule). Specifically the final text says: “States and other certifying 

entities may also use an approved WQS variance when issuing certifications under section 401 of the 

Act.” EPA interprets this language to recognize that a WQS variance may be the basis for a state’s or 

authorized tribe’s section 401 certification when that WQS variance is the applicable WQS for purposes 

of the discharge that is subject to a federal license or permit. Some commenters requested that EPA 

limit the use of WQS variances in the context of CWA section 401 certifications to NPDES permits. EPA 

concluded it was not appropriate to restrict the use of a state-adopted WQS as the applicable WQS if 

the variance was properly adopted and addressed the pollutants at issue in the relevant 401 

certification. Adoption of WQS variances is a choice, not a requirement that is made by the state or 

authorized tribe. EPA concluded the state or authorized tribe should have the discretion to decide whether 

to adopt a WQS variance and whether to apply that WQS variance in a CWA section 401 certification for 

federal permits or licenses other than NPDES permits. EPA’s decision is consistent with the purpose of 

section 401 which is to give states and authorized tribes the authority to issue certifications of federal 

licenses and permits to ensure compliance with the state’s or authorized tribe’s WQS.

Comments also expressed concern that the proposed rule “required” the adoption of a WQS variance 

before a state could issue a 401 certification that might include conditions that would require time for 

making improvements designed to meet WQS. EPA’s WQS variance rule does not require states or 

authorized tribes to adopt WQS variances. Whether to adopt a WQS variance is a decision for the state 

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or tribe to make. EPA’s rule does not restrict the ability of states and authorized tribes “to provide time 

for an applicant to submit plans, conduct studies, and implement project modification and restoration to 

bring a project into compliance with WQS” in their 401 certifications. The existing requirements of CWA 

section 401 and EPA’s implementing regulations are not changed by today’s final rule. The central 

feature of CWA section 401 is the state or authorized tribe’s ability to grant, grant with conditions, deny, 

or waive certification for federally licensed or permitted activities that may discharge into navigable 

waters. Many states and authorized tribes rely on 401 certification to ensure that federal projects do not 

cause adverse water quality impacts. By adopting a WQS variance, the state or authorized tribe lays the 

groundwork for issuing a certification (possibly with conditions, as per CWA 401(d)) that allows a federal 

license or permit to be issued as meeting applicable WQS (i.e., the WQS variance). If a state or 

authorized tribe issues a CWA 401 certification based on a WQS variance, EPA recommends that the 

state or tribe consider whether to include the applicable interim requirements from the WQS variance 

as conditions of its certification. Where a state or authorized tribe has an EPA-approved provision 

authorizing the use of CS for WQBELs in NPDES permits, it may issue a 401 certification with conditions 

that reflect its desire that a CS be issued for the federal NPDES permits. Since this is a rule of national 

scope, comments on any state-specific rule related to certification requirements is outside the scope of 

this rulemaking.

Comments questioned whether a federal entity pursuing a permit or license subject to 401 certification

needs to apply to the relevant state or authorized tribe for the WQS variance. The final rule does not 

prohibit a state or authorized tribe from submitting a WQS variance to EPA for review even where no 

permit or license applicant is applying for a WQS variance. The state or authorized tribe retains 

discretion to move forward with adoption of a WQS variance regardless of whether a federal entity has 

applied for it or not. 

Comments regarding what is allowed or prohibited under Title 40 of the Code of Federal Regulations 

(CFR) Part 121 (state certification activities requiring a federal license or permit) regulations are outside 

the scope of this rulemaking.

A comment raised the concern that the process for State adoption and EPA approval of WQS variances 

may make it infeasible for a permittee to obtain a WQS variance before the state issues a 401 

certification. This comment was made in the context of concerns that a WQS variance would be a 

prerequisite to obtaining a 401 certification. As clarified above, EPA’s final rule does not require any 

state or authorized tribe to adopt a WQS variance. A state’s or authorized tribe’s section 401 

certifications would be made on the basis for the applicable WQS which may, or may not, be a WQS 

variance. To the extent timing is a concern, EPA describes several ways that states and authorized tribes 

can structure their regulations to allow for streamlined processes for adoption and approval of WQS 

variances in section II.E of the preamble to the final rule (“What is EPA’s Position on Certain Public 

Comments?”). Additionally, this comment expressed concern about the difference in the proposed 

maximum ten-year duration of a WQS variance in relation to the possible length of some federal permits 

and licenses (e.g., 20 to 50 years). For the many reasons discussed in the preamble and response to 

comments, EPA has revised the allowed duration of a WQS variance, removing the ten-year maximum. If 

a state or authorized tribe decides to adopt a WQS variance in the context of a long-term federal permit 

or license, any such WQS variance will need to comply with the requirements for adoption of a WQS 

variance and will require EPA’s review and approval.

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EPA disagrees with the comment on CWA section 401 certification linked to EPA’s inclusion of an

additional attainability factor related to dam removal and restoration activities for justifying WQS 

variances to CWA 101(a)(2) uses (see section 131.14(b)(2)(i)(A)(2)). The commenter does not believe a 

new factor is needed for a state or authorized tribe to issue certifications “for projects that will take 

some time.” EPA discusses its rationale for including the new factor in the preamble to the proposed 

rule at 78 FR 54534-5453 (September 4, 2013). As described above, adoption of WQS variances is a 

choice, not a requirement that is made by the state or authorized tribe.

E. Current Water Quality and Downstream Protection

Commenters expressed concern about how a WQS variance affects downstream dischargers and their 

permit limits. Commenters said that a WQS variance in an upstream segment will increase the pollutant 

load in the downstream segment, potentially negatively impacting the downstream discharger(s). As 

described in subsection B of this essay, the final regulation at section 131.14(b)(1)(ii) specifically 

prohibits a WQS variance that would allow the lowering of “currently attained water quality.” Therefore, 

the upstream discharger cannot increase the load of the pollutant under the WQS variance. See EPA’s 

response to code 8.f for additional discussion on currently attained water quality. Second, EPA’s NPDES 

permit regulations include provisions at sections 122.4(d), 122.44(d)(1)(i), and 122.44(d)(4) that already 

require permit limits to account for protection of downstream WQS. Therefore, regardless of whether 

the upstream discharger has a WQS variance or not, the permitting authority of the upstream discharger 

must comply with those NPDES permit regulations. Additionally, EPA recognizes that the water quality 

associated with the WQS variance (even once the WQS variance has achieved the HAC) may still cause 

or contribute to an impact downstream during the time period of the variance. However, since a 

variance establishes a timing mechanism to ensure feasible progress is made to improve water quality 

towards meeting the underlying designated use and criteria, a variance is expected to result in 

improving water quality over time and lessening any adverse impact to downstream WQS. See also 

“Protection of Downstream Waters in WQS: Frequently Asked Questions” 

(http://water.epa.gov/scitech/swguidance/standards/library/upload/downstream-faqs.pdf).

F. Interim Requirements and National Pollutant Discharge Elimination System

Permits

With regard to comments on whether or not numeric interim requirements are necessary in a WQS 

variance and with regard to comments requesting that EPA clarify the relationship between WQS and 

municipal separate storm sewer system (MS4) permit requirements, see EPA’s response to code 8.g.ii – 

Variances Submission Requirements: Numeric Interim Requirements. In addition, to the extent that MS4 

permits include numeric WQBELs, those effluent limits must derive from and comply with the applicable 

WQS. A WQS variance would serve as the applicable WQS for the NPDES permitting purpose. EPA agrees 

in part with the comments concerning EPA’s characterization of a WQS variance as “interim 

requirements.” To address these and other comments, EPA has included a definition of “WQS variance” 

in section 131.3(o): a WQS variance is “a time-limited designated use and criterion for a specific 

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

of the WQS variance”. EPA has revised the language in section 131.14(b)(1)(ii)) to clarify that a WQS 

variance must include the requirements that apply throughout the duration of the WQS variance. 

Additionally, section 131.14(c) requires any limitations and requirements necessary to implement a 

WQS variance be included as enforceable conditions of the NPDES permit.

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G. Other

EPA disagrees with comments that WQS variances are not WQS (see EPA’s response to code 8.f.i – 

Variances Applicability: Scope).

With regard to federally promulgated variance procedures in 40 CFR section 131.34 (Kansas) and section

131.40 (Puerto Rico), EPA disagrees with the commenter’s characterization of those regulations. First, 

EPA proposed and is finalizing changes to both of those provisions so that they reference the final rule at 

section 131.14. Second, the variance procedures in those two regulations were intended to allow the 

state or territory that was the subject of the promulgation to be able to adopt WQS variances to the 

WQS that are part of the same federal promulgation. Those variance procedures do not authorize or 

prohibit the state or territory from adopting WQS variances to their own WQS. Any resulting WQS 

variance from either of the federally-promulgated variance procedures must still be adopted by the 

state or territory and submitted for review and action by EPA under CWA section 303(c).

With regard to comments on public outreach concerning WQS variances, the final rule does not direct 

states or authorized tribes to take a particular approach to notifying the public regarding the availability 

of WQS variances generally. However, whenever a state or authorized tribe adopts a WQS variance, it 

must meet the requirements for review and revising WQS, including holding a public hearing in 

accordance with section 131.20(b) and 40 CFR Part 25. 

In response to comments requesting that EPA include flexibility to develop a WQS variance for use by 

future permittees, EPA has provided clarification in section II.E of the preamble to the final rule that as 

“an alternative to identifying the specific dischargers at the time of adoption of a WQS variance for 

multiple dischargers, states and authorized tribes may adopt specific eligibility requirements in the WQS 

variance. This will make clear what characteristics a discharger must have in order to be subject to the 

WQS variance for multiple dischargers. It is EPA’s expectation that states and authorized tribes that 

choose to identify the dischargers in this manner will subsequently make a list of the facilities covered 

by the WQS variance publicly available (e.g., posted on the state or authorized tribal website).” See also 

discussion in EPA’s response to code 8.f.i – Variances Applicability: Scope.

In response to comments on nonpoint sources (NPS) and waterbody variances see EPA’s response to 

code 8.g.v – Variances Submission Requirements: Identification and Documentation of BMPs for NPS

and to code 8.f.i – Variances Applicability: Scope. 

EPA disagrees with comments suggesting “states will be required to adopt formal rules, governing the 

procedures by which variances will be reviewed and issued, creating a new burden on states...” The final 

rule does not require states and authorized tribes to have WQS variance policies or procedures. 

Therefore, there is no additional or new burden related to development and submittal of WQS variance 

policies or procedures. The final rule at section 131.14 sets the requirements for WQS variances.

However, the final rule does not prohibit states and authorized tribes from developing a WQS variance 

policy or procedure so long as such policies or procedures are not inconsistent with the final rule. See 

additional discussion in section II.E of the preamble to the final rule on this issue.

With regard to consultation and federalism impacts, see section IV of the preamble to the final rule, 

specifically sections D, E, and F.

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Essay 8.f.iii – Variances Applicability: Variances and Technology-Based 

Effluent Limits

A. General Overall Comments

The U.S. Environmental Protection Agency (EPA) appreciates comments supporting the proposal that a 

variance shall not be granted if the designated use and criterion can be achieved by implementing 

technology-based effluent limits required under sections 301(b) and 306 of the Clean Water Act (CWA) 

(proposed at Title 40 of the Code of Federal Regulations (CFR) section 131.14(a)(3)). Supporters said that 

the proposal was consistent with the CWA, and that any other interpretation would not be. EPA agrees.

Some comments expressed support in principle but questioned the need for the clarification, as in their

view, a use is attainable if it can be attained by implementing technology-based effluent limits which are 

practicable by definition. EPA’s view is that including this requirement is useful and prevents confusion

by ensuring that a minimum expectation is clear to all parties and has retained it in the final rule.

The final rule specifies at section 131.14(a)(4): “A State may not adopt WQS variances if the designated 

use and criterion addressed by the WQS variance can be achieved by implementing technology-based 

effluent limits required under sections 301(b) and 306 of the Act.” The final rule also contains the 

following definition at section 131.3(h): “Water quality limited segment means any segment where it is 

known that water quality does not meet applicable water quality standards, and/or is not expected to 

meet applicable water quality standards, even after the application of the technology-based effluent 

limitations required by sections 301(b) and 306 of the Act.” 

Some commenters requested that EPA should expressly provide in this subpart that States must only 

consider whether EPA-promulgated national effluent limitations guidelines (ELGs) could eliminate the 

need for the requested variance and further provide that States need not undertake a case-specific best 

professional judgment analysis to fulfill the proposed standard set out in section 131.14(a)(3). EPA 

considers “technology-based effluent limits required under section 301(b)” to include existing permit 

effluent limitations whether derived based on a nationally promulgated ELGs or, in the absence of a 

promulgated ELG, derived based on best professional judgement (BPJ). Congress intended that permits 

include technology-based effluent limits whether based on an ELG or BPJ. EPA understanding of 

Congress’ intent is reflected in 40 CFR Part 125, specifically section 125.3(a) and (c) which state that 

“technology-based effluent limits under Section 301(b) of the Act represent the minimum level of 

control that must be imposed in a permit...” and establishes the methods for imposing technologybased requirements by providing three approaches: ELGs, case-by-case BPJ, or a combination of ELGs 

and BPJ. If compliance with current technology-based permit limits would attain water quality standards 

(WQS), a variance would not be needed or appropriate. See

http://water.epa.gov/polwaste/npdes/basics/Water-Quality-and-Technology-Based-Permitting.cfm. 

Technology-based effluent limits required under CWA section 306, are new source performance 

standards (NSPS). In the absence of EPA-promulgated NSPS, permitting authorities do use BPJ to derive 

NSPS. But when permits have effluent limits based on NSPS, a variance would not be appropriate if WQS 

would be attained by implementation of those NSPS effluent limits.

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EPA also notes that the footnote regarding the “Hanlon Memorandum” cited in a number of comments

is not relevant to the technology-based effluent limit provision in the WQS variances section of the final 

rule in section 131.14.

In regards to the exception described by one commenter where EPA promulgates a “best available 

technology [economically achievable]” (BAT) ELG with allowance of an extended period of compliance 

and the facility cannot meet its water quality-based effluent limit (WQBEL) until its BAT technology is in 

place, EPA does not agree that a WQS variance is the appropriate tool. In this circumstance a National 

Pollutant Discharge Elimination System NPDES permit compliance schedule (CS) for the WQBEL may be 

the appropriate tool to allow time install the technology. See section II.E of the preamble to the final 

rule for additional discussion on difference between WQS variances and (NPDES) permit CS. 

EPA disagrees that the final regulation should consider the cost impact with regard to technology-based 

requirements by adding the phase “economically feasible.” The final regulatory requirement does not 

contain this phrase as it is unnecessary. The final rule is consistent with the basic CWA requirements 

regarding technology-based effluent limitations, which include economic considerations and do not 

require implementation of “any technology.” Technology-based limitations for existing sources are 

based on best available economically achievable technologies. For information about technology based 

limits under the CWA, see 

http://water.epa.gov/polwaste/npdes/basics/Water-Quality-and-Technology-Based-Permitting.cfm. 

A commenter states that the rule should specify that a WQS variance cannot be adopted if the water 

quality criterion can be achieved with a combination of technology-based requirements and/or

aggressive permit requirements for best management practices (BMPs) such as low impact development 

for new development and retrofits for existing sources. EPA explained its position above regarding 

issuance of variances when WQS can be attained by implementing required technology-based effluent 

limitations. Regarding requiring “aggressive permit requirements” for the BMPs mentioned by the 

commenter, EPA’s position is that it is not appropriate to include such a provision in this WQS 

regulation. The NPDES permitting program will determine and implement the appropriate effluent 

limitations, including any BMPs for point sources. In addition, the final rule encourages the use of BMPs

via a pollutant minimization program (PMP) for WQS variances (see section II. E of the preamble to the 

final rule for a discussion of PMPs) and, in fact, requires a PMP when establishing the highest attainable 

condition (HAC) for the situation where there is no feasible pollution control technology. Additionally,

EPA expects permit writers to avail themselves of the information that a state or authorized tribe

provides in the WQS variance and supporting documentation regarding the actions that justify the 

length of the WQS variance. Specifically, the final rule at section 131.14(b)(2)(ii) specifies: 

“Documentation demonstrating that the term of the WQS variance is only as long as necessary to 

achieve the highest attainable condition. Such documentation must justify the term of the WQS variance 

by describing the pollutant control activities to achieve the highest attainable condition, including those 

activities identified through a Pollutant Minimization Program, which serve as milestones for the WQS 

variance.” Permit writers can use this information as a source of milestones for permit terms and 

conditions that derive from the WQS variance. Further, regarding where nonpoint sources (NPS) are 

contributing to the pollution challenge that the WQS variance is intended to address and the state or 

authorized tribe is able to work with all stakeholders to adopt a WQS variance applicable to a water 

body or waterbody segment, the final rule requires identification and documentation of the NPS BMPs 

(section 131.14 (b)(2)(iii)). Commenters supporting inclusion of BMPs in permits before allowing a WQS 

variance said that EPA should not promulgate rules that are a disincentive to consistent forward 

progress on improving water quality and meeting WQS. EPA does not agree that such a requirement is

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necessary because EPA’s stated goal in regards to WQS variances and the provisions in section 131.14

are designed to lead to incremental progress towards the CWA goal of maintaining and restoring the 

chemical, physical and biological integrity of the nation’s waters.

Some commenters provided anecdotal examples of a state without NPDES authority that has not 

adopted variances as WQS revisions but rather through a coordinated EPA/state permitting process, and 

said that the current process should not have to be changed because it is unnecessary and burdensome. 

For comments regarding the need for EPA approval and disapproval of variances as WQS and possible 

coordination with the NPDES permitting process or other ways to streamline the administrative process, 

see EPA’s response to code 8.f.i. – Variances Applicability: Scope and section II.E of the preamble to the 

final rule.

Some commenters said that the proposal regarding variances and need to implement technology-based 

effluent limits should be the minimum regulatory requirements for granting a variance. That states and 

authorized tribes should retain discretion on granting and adopting variances. EPA agrees that the final 

requirement regarding technology-based limits must be met at a minimum, before granting a variance, 

but there are other conditions that are necessary to ensure the WQS variance process has a sufficient 

level of accountability, transparency, and flexibility. EPA’s view is that the final rule provides a structured 

approach to variances that still allows some state and authorized tribal discretion. See section II.E of the 

preamble to the final rule for EPA’s rationale for its approach for WQS variances.

For comments regarding the difference between the operational definition of WQS variances as “a time 

limited designated use and criterion” the characterization of WQS variances as “interim requirements,” 

see EPA’s response to code 8.f.ii – Variances Applicability: Approved Variances and Permitting and 

303(d).

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Essay 8.g – Variances: Submission Requirements

A. Specific Revisions to Rule Language

The U.S. Environmental Protection Agency (EPA) disagrees with commenters suggesting replacement of 

the words: “Submission Requirements” with “Minimum requirements of a WQS variance:” or 

“documentation requirements.” A water quality standards (WQS) variance is a WQS requiring EPA 

review and approval or disapproval. The suggested revision could be interpreted as states and 

authorized tribes not needing to submit the WQS variance to EPA for review and approval and confuse 

the public. See Response to comment topic 8.c for discussion of why a WQS variance is a WQS subject to 

EPA review and approval or disapproval. 

B. General Submission Requirement

EPA disagrees with commenters that said EPA should not specify submission requirements for a WQS 

variance. As discussed in the preamble of the proposed rule, the EPA has heard from states, tribes, and 

stakeholders that there is confusion, inconsistency, and mixed interpretations about how, when, and 

where variances may be used appropriately. The final rule provides more specificity and clearer 

requirements on the development and use of variances. The final rule also provides requirements to 

ensure that WQS variances are used appropriately. Such regulations will provide regulatory certainty to 

states and authorized tribes, the regulated community, and assure the public that WQS variances will 

facilitate progress toward attaining designated uses. When all parties are engaged in a transparent 

process pursuant to these regulations, states and authorized tribes can move past traditional barriers 

and begin efforts to maintain and restore waters. Including submission requirements in the final rule is 

an important part of achieving this goal.

C. General Support

EPA thanks commenters supporting EPA’s goal of provides more specificity and clearer requirements on 

the development and use of WQS variances. 

D. General Support for Water Quality Standards Variance Limitations 

including 10-Year Term Limit

Although EPA eliminated a specific limit for any single WQS variance term, the final rule instead contains 

several provisions to insure that WQS variances will be used to facilitate progress toward attaining 

designated uses. See comment response topic 8.g.iii for discussion of WQS variance expiration dates.

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Essay 8.g.i – Variances Submission Requirements: Identifying 

Information

A. General Support

The U.S. Environmental Protection Agency (EPA) thanks the commenter for supporting the identification 

requirements of the final rule. 

B. Definition of Pollutant Minimization Program

In response to commenters that suggested EPA better define the term “pollutant minimization program

(PMP),” EPA now includes in the final rule the definition of PMP at section 131.3(p). The final rule states 

that a PMP, in the context of section 131.14, is a structured set of activities to improve processes and 

pollutant controls that will prevent and reduce pollutant loadings. In the preamble, EPA further explains 

that pollutant control technologies represent a broad set of pollutant reduction options, such as process 

or raw materials changes and pollution prevention technologies, practices that reduce pollutants prior 

to entering the wastewater treatment system, or best management practices (BMPs) for restoration and 

mitigation of the water body. 

C. Replace “Submission” with “Minimum” 

EPA disagrees with commenters suggesting to replace the word “Submission” with the word “Minimum” 

in section 131.14(b) because it is important to ensure that states and authorized tribes understand that 

a water quality standards (WQS) variance is a WQS requiring EPA review and approval or disapproval.

The suggested revision could be interpreted by states and authorized tribes as not needing to submit 

the WQS variance to EPA for review and approval. See response to EPA’s response essay 8.g for 

additional information on submission requirements. See also EPA’s essays for 8.c and 8.f.i for discussion 

of why a WQS variance is a WQS subject to EPA review and approval or disapproval.

D. Any Water Quality Standards Variance Must Specify a Water Body or 

Waterbody Segment

EPA appreciates commenters suggested editorial changes that sought to ensure that any WQS variance 

identify the water body or waterbody segment to which it applies. EPA never intended to provide for a 

WQS variance that does not identify the water body or waterbody segment to which the WQS variance 

applies. The rule language was revised to clarify that any WQS variance must identify the water 

body/waterbody segment(s) to which the WQS variance applies (see section 131.14(b)(1)(i)).

E. Transparency

See response topic 8.l for a discussion on how the final rule provides the transparency and 

accountability needed to ensure that WQS variances are used appropriately.

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F. Renewal for Waterbody Variances

See response topics 8.i and 8.g.v for discussion of WQS renewal requirements and nonpoint source

(NPS) BMPs related to WQS variances applicable to a water body or waterbody segment.

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Essay 8.g.ii – Variances Submission Requirements: Numeric Interim 

Requirements

A. General Support

The U.S. Environmental Protection Agency (EPA) notes that several commenters support the final rule’s 

requirement that states and authorized tribes must specify a quantifiable highest attainable condition 

(HAC).

B. Eliminate the Requirement to Express the Highest Attainable Condition 

Numerically Because It Is Incompatible with Water Quality Standards

Variances for Combined Sewer Overflows or Other Weather-Related 

Discharges

EPA notes that several commenters said EPA should eliminate the requirement that the HAC of a water 

quality standards (WQS) variance be specified numerically because it could be difficult or impossible to 

estimate effluent quality associated with combined sewer overflows (CSOs) or other weather-related 

events. EPA agrees that numerically estimating effluent quality associated with CSOs or other weatherrelated events can be impractical. EPA never intended to require states and authorized tribes to 

necessarily estimate the concentration of pollutants associated with a WQS variance in ambient water 

or effluent. EPA expects states and authorized tribes will choose to specify the HAC of a WQS variance as 

the concentration of a pollutant or pollutant parameter for many WQS variances because concentration 

is often a relatively stable measure of the pollutant or pollutant parameter in a discharge, and thus will 

likely be the method the permitting authority uses to specify the water quality-based effluent limit 

(WQBEL) is a National Pollutant Discharge Elimination System (NPDES) permit. However, EPA recognizes 

there may be cases were specifying the HAC as a concentration may not adequately characterize the 

discharge resulting in nonattainment of WQS. The final rule provides states and authorized tribes with

the flexibility to express the HAC as numeric pollutant concentrations in ambient water, numeric 

effluent conditions, or other quantitative expressions of pollutant reduction. Examples of expressing the 

HAC with regard to CSOs include a maximum number of overflows, a percentage of time attaining the 

underlying designated use, and high flow/velocity cutoffs suspending a WQS. See: “Guidance: 

Coordinating CSO Long-Term Planning with Water Quality Standards Reviews” (EPA-833-R-01-002, 

July 31, 2001). An example of expressing the HAC with regard to selenium infiltration during wetweather events includes a percent reduction in selenium concentration or load. As the commenter 

stated the state would also include pollutant minimization practices in the justification for duration of 

the WQS variance. 

Because EPA’s objective is to ensure a WQS variance results in measureable progress toward the 

underlying designated use, EPA replaced the word “numeric” in the proposed rule with the term 

“quantifiable expression” in the final rule to clarify EPA’s intended flexibility for expressing the HAC. 

The requirement to specify a quantifiable expression of the HAC is an important feature of a WQS 

variance that facilitates development of NPDES permit limits and requirements and allows states, 

authorized tribes, and the public to track progress toward the ultimate goal of attaining the underlying 

designated use. 

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C. Eliminate the Requirement to Express the Highest Attainable Condition 

Numerically Because It Is Incompatible with Municipal Separate Storm Sewer

System Permits That Are Based on Best Management Practices 

As described in subsection B of this essay, the final rules requires states and authorized tribes to provide 

a quantifiable expression of the HAC. This requirement is an important feature of a WQS variance that 

facilitates development of NPDES permit limits and requirements and allows states, authorized tribes, 

and the public to track progress. Some commenters said EPA should eliminate the requirement that the 

HAC of a WQS variance be specified numerically because such a requirement limits the applicability of 

WQS variances for stormwater discharges under municipal separate storm sewer system (MS4) permits.

Clean Water Act (CWA) section 402(p)(3)(B)(iii) provides that stormwater permits for MS4 discharges 

“shall require controls to reduce the discharge of pollutants to the maximum extent practicable ... and 

such other provisions as the Administrator or the State determines appropriate for the control of such 

pollutants.” Under this provision, the NPDES permitting authority has the discretion to include 

requirements for reducing pollutants in stormwater discharges as necessary for to meet WQS. At the 

outset of both the Phase I and Phase II stormwater permit programs, EPA provided guidance on the type 

of WQBELs that were considered most appropriate for stormwater permits. See Interim Permitting 

Policy for Water Quality-Based Effluent Limitations in Storm Water Permits (61 FR 43761, August 26, 

1996; 61 FR 57425, November 6, 1996) and the Phase II rulemaking preamble 64 FR 68753 (December 8, 

1999). Under the approach discussed in these documents, EPA envisioned that in the first two to three 

rounds of permit issuance, stormwater permits typically would require implementation of increasingly 

more effective best management practices (BMPs). In subsequent stormwater permit terms, if the BMPs 

used during prior years were shown to be inadequate to meet the attainment of applicable WQS, the 

permit would need to contain more specific conditions or limitations.

EPA’s November 26, 2014 memorandum: “Revisions to the November 22, 2002 Memorandum: 

‘Establishing Total Maximum Daily Load (TMDL) Wasteload Allocations (WLAs) for Storm Water Sources 

and NPDES Permit Requirements Based on LA’s’” provides guidance on how to include clear, specific, 

and measurable NPDES permit requirements and, where feasible, numeric effluent limitations, in NPDES 

permits for stormwater dischargers. NPDES authorities have significant flexibility in how they express 

numeric limits in MS4 permits in addition to end-of-pipe limits, such as specifying on-site stormwater 

retention volume or percentage or amount of effective impervious cover. Numeric limits in MS4 permits 

can also be expressed as system-wide requirements rather than as individual discharge location 

requirements such as effluent limitations on discharges from individual outfalls. To ensure 

section 131.14 is consistent with EPA regulation and policy on MS4 permits for stormwater discharges, 

EPA replaced the word “numeric” with the term “quantifiable expression” to clarify that states and 

authorized tribes have the flexibility to express the HAC of a WQS variance for an MS4 discharger a 

manner appropriate for MS4 permits.

D. Eliminate the Requirement That the Highest Attainable Condition Be 

Expressed Numerically

As discussed in subsection B of this essay, the final rules requires states and authorized tribes to provide 

a quantifiable expression of the HAC. 

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EPA agrees that narrative criteria can augment numeric criteria in protecting designated uses, especially 

when pollutants cannot be precisely measured. The CWA recognizes the importance of expressing 

chemical criteria in numeric form by requiring State adoption of numeric criteria for toxic pollutants (see 

CWA section 303(c)(2)(B)). NPDES permit limits must derive from and comply with WQS. The permitting 

authority needs to translate a narrative WQS to derive a WQBEL or other permit conditions or 

requirements. Numeric criteria facilitate development of appropriate NPDES permits by providing the 

permitting authority with a more straightforward basis to determine WQBELs that derive from and 

comply with WQS.

EPA believes commenters have interpreted the term “numeric” to mean that EPA expects states and 

authorized tribes to express the HAC in all cases as a concentration of a pollutant or water quality 

parameter. This interpretation is incorrect. Although expressing the HAC as the concentration of a 

pollutant or water quality parameter will be appropriate in some circumstances, EPA recognizes that it 

may not be appropriate in other circumstances. EPA replaced the word “numeric” with the term 

“quantifiable expression” so that the final rule now requires states and authorized tribes to provide a 

quantifiable expression of the HAC. 

Some commenters expressed concern that: “if the timeline of a variance is developed to attain the use 

and/or criterion (or the highest attainable use/and or water quality) at the end of the variance period, 

then logically the water body will be out of compliance with the interim use and criterion for much of 

the term of the variance until the final state is reached. In situations where longer term variances are 

used, this creates an untenable compliance situation for states and dischargers.” These comments 

suggest confusion between WQS variances and NPDES permit compliance schedules (CS). The preamble 

to the final rule explains that a WQS variance can be appropriate to address situations where it is known 

that the designated use and criterion are unattainable today, but progress could be made toward 

attaining the designated use and criterion, whereas a permit CS may be appropriate when the permittee 

needs additional time to modify or upgrade treatment facilities in order to meet its WQBEL based on the 

applicable WQS. The preamble of the final rule further explains that a permit authority could also grant 

a permit CS when the permittee needs additional time to meet its WQBEL based on the applicable WQS 

variance such that a schedule and resulting milestones will lead to compliance with the effluent limits 

derived from the WQS variance “as soon as possible.” If a WQS variance is about to expire and a state or 

authorized tribe concludes the underlying designated use is now attainable, it is not appropriate for the 

state or authorized tribe to adopt a subsequent WQS variance. However, if a permittee is unable to 

immediately meet a WQBEL consistent with the now attainable WQS, and the permitting authority can 

specify an enforceable sequence of actions that would result in achieving the WQBEL, the permitting 

authority could grant a permit CS consistent with section 122.47. If the underlying designated use is still 

not attainable, the state or authorized tribe can adopt a subsequent WQS variance.

EPA disagrees with commenters that say EPA cannot require expression of the HAC numerically (i.e., as a

quantifiable expression) because NPDES effluent limitations are not required to be numeric. First, the

final rule does not change, and stands alone from, the permitting regulations at Title 40 of the Code of 

Federal Regulations (CFR) Part 122. Second, the final rule itself recognizes the potential for non-numeric 

permit conditions and requirements by specifying an option to express the HAC in a manner that 

includes the adoption and implementation of a pollutant minimization program (PMP), specifying in 

section 131.14(c) that any [emphasis added] limitations and requirements necessary to implement the 

WQS variance shall be included as enforceable conditions of the NPDES permit for the permittee(s) 

subject to the WQS variance, and explaining in the preamble that the permitting authority must use any

PMP included in a WQS variance to derive NPDES permit limits and requirements. 

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One commenter also stated support for that variances must specify (1) the highest attainable interim 

use and numeric criterion that apply during the term of the variance, OR (2) an interim numeric effluent 

condition that reflects the HAC for the permittee during the term of the variance. For the same reasons 

EPA has explained in this essay, EPA changed from “numeric” to “quantitative expression.” 

E. Allow Expression of the Highest Attainable Condition as a Pollutant 

Minimization Program or Narrative Standard

Commenters said EPA should allow states and authorized tribes to specify a PMP or narrative WQS as 

the HAC of a WQS variance. Identification and implementation of a PMP can be an important part of a 

WQS variance that ensures the WQS variance results in the maximum pollutant reduction achievable

during the term of the WQS variance. For example, the final rule provides that, for discharger-specific 

WQS variances, if no additional feasible pollutant control technology can be identified, the HAC can be 

expressed as the interim criterion or interim effluent condition that reflects the greatest pollutant 

reduction achievable with the pollutant control technologies installed at the time the State adopts the 

WQS variance, and the adoption and implementation of a PMP (a similar provision exists for WQS 

variances applicable to a water body/waterbody segment). However, EPA does not agree with 

commenters that suggest a WQS variance need not specify the HAC that is not in some way quantitative. 

An NPDES permit will include monitoring requirements for the pollutant(s) or pollutant parameter(s) 

with a WQBEL, and EPA sees no reason a discharger could not characterize its current effluent condition 

quantitatively on the basis of the monitoring data associated with NPDES permit compliance.

Characterizing the HAC as both the interim effluent condition (or interim criterion) that reflects the 

greatest pollutant reduction achievable with the pollutant control technologies installed at the time the 

state or authorized tribe adopts the WQS variance, and the adoption and implementation of a PMP 

meets EPA’s goal for the HAC to be both quantifiable and future reaching to drive progress towards the 

underlying WQS.

F. Identification of the Highest Attainable Condition Is Unnecessary Burden on 

States

Commenters expressed concern that requiring identification of the HAC in a WQS variance would 

impose an unnecessary burden on a state. While the new requirement to identify the HAC may impose 

some burden, EPA does not agree that it is unnecessary. In fact it is a critically important element of 

ensuring that variances achieve the purpose intended to improve water quality with the ultimate goal 

being to attain designated uses and criteria that reflect the objectives and goals of the CWA. For EPA’s 

estimates of burden related to identifying the HAC, see the final Economic Assessment in the docket for 

the rulemaking. The CWA specifies a national goal at section 101(a) to restore and maintain the 

chemical, physical and biological integrity of the Nation’s waters and an interim goal in section 101(a)(2) 

that, “wherever attainable,” water quality provide for the protection and propagation of fish, shellfish, 

and wildlife and provides for recreation in and on the water. The regulation of WQS variances in the final 

rule is consistent with the “restore” and “wherever attainable” aspects of these goals because WQS

variances are intended to allow incremental environmental progress toward the ultimate goal of 

attaining the underlying designated use. 

The purpose of a WQS variances is to provide states and authorized tribes with time to make 

incremental progress towards attaining a designated use that is not immediately attainable but may be 

attainable in the future. Making incremental progress, however, requires an understanding of what is 

incrementally attainable. The final rule facilitates incremental progress by requiring states and 

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authorized tribes to identify what is incrementally attainable in the time period the state or authorized 

tribe specifies will be the term of the WQS variance, and to set it as the goal of the WQS variance. The 

final rule refers to this incremental goal as the HAC. For discussion on the meaning of HAC, see response 

Essay 8.c. The final rule requires a state or authorized tribe to identify the HAC and to specify in the WQS 

variance the HAC as the water or effluent quality goal to be achieved by the end of the WQS variance 

term for discharger-specific WQS variances (and as the interim use and criterion for WQS variances 

applicable to a water body or waterbody segment). Identifying the HAC and specifying the HAC as the 

incremental goal of the WQS variance facilitates development of NPDES permit limits and requirements, 

and allows states, authorized tribes, and the public to track progress toward the ultimate goal of 

attaining the underlying designated use.

G. EPA Should Allow Water Quality Standards Variances for Water 

Conservation and Recycling Activities

Comment was made that EPA should expand the availability of WQS variances via the new restoration 

factor proposed at section 131.14(b)(2)(ii) that read: “Actions necessary to facilitate restoration through 

dam removal or other significant wetland or stream reconfiguration activities...” to include water 

conservation and recycling activities. EPA did revise the proposed new restoration factor in the final 

rule. EPA added the word “lakes” such that section 131.14(b)(2)(i)(A)(2) now reads: “Actions necessary 

to facilitate lake, wetland, or stream restoration through dam removal or other significant 

reconfiguration activities...” However, EPA did not include water conservation and recycling activities to 

this provision because there are other factors in section 131.10(g), which are incorporated by reference 

into section 131.14, that are adequate to cover the need for a WQS variance based on water 

conservation or recycling activities, for example, the factors related to reduced flows or human caused 

conditions.

H. EPA Should Allow the Highest Attainable Condition to Be Expressed 

Narratively

As discussed in subsection D of this essay, EPA agrees that narrative criteria can augment numeric 

criteria in protecting designated uses, especially when pollutants cannot be precisely measured.

However, EPA disagrees with commenters who said the final rule should allow states and authorized 

tribes to express the HAC using narrative statements only. The CWA recognizes the importance of 

expressing chemical criteria in numeric form by requiring State adoption of numeric criteria for toxic 

pollutants (see CWA section 303(c)(2)(B)). NPDES permit limits must derive from and comply with WQS.

A permitting authority needs to translate a narrative WQS to derive a WQBEL or other permit conditions 

or requirements. Quantitative expressions facilitate development of appropriate NPDES permits by 

providing the permitting authority with a more straightforward way to determine WQBELs that derive 

from and comply with WQS.

I. Clarification on Pollution Minimization Program 

EPA thanks commenters who noted that the term PMP is not clearly defined. EPA now defines PMP in 

the final rule now at section 131.3(p). See response Essay 8.g.i for additional discussion on the definition 

of PMP.

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J. It Is Unclear How EPA’s Proposed Variance Requirements Would Apply to 

Narrative Criteria

Commenters said the regulation should allow a narrative expression of the HAC because they currently 

do not set interim numeric criteria or numeric effluent limits in their WQS variances, and believe that 

requiring a numeric expression of the HAC for uses that currently have narrative criteria such as 

nutrients are inconsistent with allowing narrative criteria in WQS. Commenters also said requiring a 

numeric expression of the HAC is generally inconsistent with narrative criteria. EPA disagrees with these 

comments.

As discussed in subsections B and D of this essay, EPA revised the final rule to (1) require a quantifiable 

expression of the HAC, and (2) where there is no additional feasible pollutant control technology that 

can be identified, to allow the HAC to be expressed with a quantitative component that reflects the 

greatest pollutant reduction achievable with the pollutant control technologies installed at the time the 

state or authorized tribe adopts the WQS variance plus the adoption and implementation of a PMP. EPA 

has determined that a quantifiable expression of the HAC is necessary and important even for narrative 

criteria because such an expression helps ensure that there will be water quality improvements (a key 

purpose of a variance) during the term of the variance. For pollutants with narrative criteria, the state or 

authorized tribe can perform studies during the analysis to support the justification of the WQS variance 

to identify, for example, the current level of water quality and a percent reduction that is achievable 

during the term of the WQS variance and use that information to articulate a “quantifiable expression” 

in the WQS variance. In the scenario where there is no additional feasible pollutant control technology 

that can be identified, EPA expects the state or authorized tribe to identify the current water quality 

levels (including optimization of current pollutant control technologies) and use that information to 

provide the quantifiable piece of the expression along with the adoption and implementation of a PMP.

K. Reference to Interim Conditions Encroaches on State Primacy and Could Be 

Interpreted to Authorize Conditions on Land Use and Nonpoint Sources, 

Exceeding EPA’s Clean Water Act Authority

Commenters said: “As drafted, the reference to interim conditions that EPA could impose encroaches on 

state primacy and could be interpreted to authorize conditions on land use and nonpoint sources, 

exceeding EPA’s CWA authority”. The final rule does not authorize EPA to impose interim conditions. A 

state or authorized tribe identifies and adopts “requirements that apply throughout the term of the 

variance” that will achieve the HAC by the end of the variance term. The final rule at section

131.14(b)(1)(ii) provides the options available for a state or authorized tribe to articulate the HAC. Once 

the WQS variance is approved by EPA, the HAC identified and adopted by the state or authorized tribe is

the applicable WQS for CWA section 402 permitting and for issuing 401 certifications. EPA’s authority is 

to review and approve or disapprove the WQS variance as provided by CWA section 303(c). With respect 

to nonpoint sources (NPS), EPA’s rule simply provides that for WQS variances applicable to a water body 

or waterbody segment, states’ and authorized tribes’ submissions must include identification and 

documentation of any cost-effective and reasonable BMPs for NPS. The regulation does not authorize 

EPA to compel enforcement of NPS controls. For additional discussion on WQS variances and NPS BMPs, 

see response Essay 8.g.v. For a discussion regarding state primacy, see response Essay 3a.

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L. The Rule Should Specify That the Highest Attainable Condition Is 

Determined by the State or Authorized Tribe in Order to Avoid Litigation

Commenters suggest the final rule should specify that the HAU and criteria and the HAC “are 

determined by the state based on data and information that the state determines is best available.” 

Commenters also said that the HAC concept is “an invitation for litigation.” EPA disagrees with the 

changes requested by the commenters. EPA also disagrees with commenters suggesting that EPA should 

include in the definition of a WQS variance that specifies the HAC as the “condition during the specified 

time period that the State determines is highest attainable.” Based on these and other comments, EPA 

did revise the definition of HAU to better link the definition to the state’s or tribe’s analysis in the use 

attainability analysis (UAA) (see revised definition at 131.3(m) and also response Essay 5.e for more 

discussion on the definition of HAU). For information on EPA’s rationale on why the Agency did not and 

has not defined HAC in the same way as HAU, see response Essay 8.c. EPA notes that the final rule 

provides a variety of options for states and tribes to articulate the HAC. EPA disagrees that the 

expression of HAC, based on the final rule, will result in increased litigation. While the states and 

authorized tribes have an critical role in the adoption of WQS variances, it is EPA’s position that the 

requirements included in the final rule regarding adoption of the HAC are important to ensuring 

essential considerations are taken into account in adopting WQS variances and that all states and tribes 

operate under the same set of requirements.

To the extent the commenters are suggesting that the rule should specify states and authorized tribes 

have sole authority to identify the HAC for WQS variances, EPA cannot agree. A WQS variance is a

revised WQS subject to EPA review and approval or disapproval, requires a public process, and must be 

reviewed on a triennial basis. To ensure the process is subject to minimum requirements designed to 

protect both the outcome and process, EPA’s position is that the requirements in the final rule are 

necessary. Deferring to state and tribal discretion without such minimum requirements as set forth in 

the final rule, would diminish the important roles to be played by the public and EPA. The CWA assigns

EPA an oversight role of reviewing and approving or disapproving state and authorized tribal WQS (CWA 

section 303(c)). EPA’s position that the requirements in the final rule are needed to ensure an outcome 

that will advance the intended purpose of a WQS variance – to improve water quality – and to have 

objective requirements on which EPA and the public can evaluate whether that outcome is met.

M. Water Quality Standards Variance Renewal

Commenters expressed concern that a variance renewal will be denied “if the applicant did not comply 

with the conditions of the original WQS variance.” This issue is addressed in response Essay 8.i.

N. Expiration Date of a Water Quality Standards Variance

Commenters said the rule should allow the state to specify the expiration date of a WQS variance “as 

the State determines the WQS can be met.” EPA disagrees with this comment. WQS variances should 

not be open ended and should specify an end date based on the underlying analysis. However, in the 

final rule EPA no longer specifies a federal maximum term for a WQS variance. States and authorized 

tribes must justify the duration and provide supporting documentation. See also response to Essay 8.g.iii 

for more discussion on the expiration date issue.

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O. Seasonal Water Quality Standards Variances

The final rule does not prohibit a “seasonal variance.” If a state or authorized tribe demonstrates that 

the underlying designated use is not attainable during a particular time of year, then a WQS variance 

during the time of year when the designated use is not attainable would be appropriate provided that 

the WQS variance meets the requirements of section 131.14. One of the requirements specified in 

paragraph (b)(1)(ii) provides that the state or authorized tribe must specify a quantifiable expression of 

the HAC of the water body or waterbody segment. In this case, one quantifiable component of the HAC

would be time period during which the interim requirements of the WQS variance are in effect. 

However, where the seasonal WQS challenge is not expected to be improved or resolved over time, it 

may be more appropriate for states and authorized tribes to revise their WQS to reflect a seasonal use 

change.

P. Levels Currently Achievable plus a Pollutant Minimization Program

Commenters suggested that EPA clarify that in situations where no feasible wastewater treatment 

option can be identified to meet the designated use and the state or authorized tribe expresses the HAC 

as the levels currently achievable and a requirement to develop and implement a PMP, identification of

a feasible wastewater treatment option need only take place at the time the state adopts the WQS 

variance.

To clarify when and how states and authorized tribes may utilize a WQS variance in such situations, EPA 

revised the proposed rule in a couple of ways. First, EPA moved the language describing the option to 

express the HAC as the levels currently achievable and a requirement to develop and implement a PMP

from the preamble of the rule to the regulatory text. Specifically, EPA revised the regulatory text to 

clarify that in situations where no additional feasible pollutant control technology can be identified, the 

HAC may be expressed for discharger-specific WQS variances as an interim criterion or interim effluent 

condition (and for WQS variances applicable to a water body or waterbody segment as the interim use 

and interim criterion) that reflects the greatest pollutant reduction achievable with the pollutant control 

technologies installed at the time the State adopts the WQS variance [emphasis added], and the 

adoption and implementation of a PMP. Second, EPA included the definition of PMP in the final rule text 

at 131.3(p).

A WQS variance specifying the HAC in this manner can provide a mechanism for states and authorized 

tribes to retain a designated use that is not attainable even when all feasible pollutant control options 

are currently exhausted, but a state or authorized tribe believes that feasible pollutant control options 

may become available in the future. However, this does not mean a state or authorized tribe can use a 

WQS variance to maintain the status quo indefinitely. The discharger(s) subject to such a WQS variance 

not only must adopt and implement a PMP, but the final regulation at sections 131.14(b)(1)(iv) and 

131.14(b)(2)(ii) requires the term of any WQS variance to only be as long as necessary to achieve the 

HAC, and 131.14(b)(2)(ii) further requires the state or authorized tribe to justify the term of any WQS 

variance by describing the pollutant control activities that will be implemented to achieve the HAC, 

including those activities identified through a PMP. This means the state or authorized tribe must specify 

a WQS variance term that is no longer than the time that can be reasonably justified to complete the 

pollutant control activities specified in the PMP. This is a reasonable position since a WQS variance is 

time-limited and states and authorized tribes can obtain a subsequent WQS variance if the underlying 

use and criteria continue to be unattainable and more progress toward the underlying WQS can be 

made (and meeting any other of the requirements of section 131.14). The time needed to complete the 

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pollutant control activities specified in the PMP must reflect either the time needed to plan an action, 

time to implement an action, or time to evaluate the outcome of an action. If, after the term of the WQS 

variance, the state or authorized tribe finds that the underlying designated use is still not attainable, the 

state or authorized tribe may adopt a subsequent WQS variance consistent with the requirements of 

section 131.14 (which may include new pollutant minimization strategies or newly available pollutant 

control options). A commenter asked what happens if all pollutant minimization options are exhausted.

If this is truly the case, EPA notes that use removal is still an option under the regulations.

Q. Variances Should Not Have a Time Limit

EPA disagrees with commenters that said EPA should not require a time limit for WQS variances. A WQS 

variance is defined in section 131.3(o) as a time-limited designated use and criterion for a specific 

pollutant(s) or water quality parameter(s) that reflect the HAC during the term of the WQS variance. In 

order to promote consistency and clarity and to ensure that WQS variances are truly time-limited, the 

final rule requires states and authorized tribes to specify the term of the WQS variance expressed as an 

interval of time from the date of EPA approval or a specific date. However, EPA eliminated the ten year 

maximum WQS variance term in the proposed rule. Instead, the final rule requires states and authorized 

tribes specify the duration of the WQS variance (i.e., by providing an expiration date) only as long as 

necessary to achieve the HAC and consistent with the demonstration provided in section 131.14(b)(2). 

See comment response topic 8.g.iii for more discussion about the term of a WQS variance.

R. Needlessly Complicates and Extends the Permitting Process

Commenters said: “the requirement to identify the highest attainable interim use and related specific 

interim numeric limit needlessly complicates and extends the permitting process by requiring a 

preliminary study to make these findings rather than focusing on the crux of the issue-the determination 

as to whether a long-term site specific standard is appropriate.” As discussed in section II.E of the 

preamble to the final rule and in response Essay 8.c., EPA revised its approach regarding the articulation 

of the HAC in order to simply the options. For example, for discharger-specific variances, EPA no longer 

includes the HAC to be articulated as the interim use and interim criterion and instead allows three 

options.

S. Should Require Both Effluent and Ambient Highest Attainable Condition

Commenters suggested that the rule should require identification of both a numeric criterion and 

numeric effluent condition. Both ways of expressing the HAC are appropriate but EPA’s position is that it 

is not necessary that the HAC must be expressed in both ways. In light of that position, EPA concluded it 

was appropriate to provide states and authorized tribes the flexibility to pick just one way of expressing 

the HAC if that was their choice. Of course they could choose to express the HAC in both ways. See 

section II.E of the preamble to the final rule for a discussion of EPA’s rationale on the options for 

articulation of HAC and it rationale that interim criteria and interim effluent conditions are reasonable 

surrogates for the interim use and criterion. States and authorized tribes often adopt discharger-specific 

WQS variances because requiring the discharger to meet the WQBEL of the NPDES permit would result 

in substantial and widespread economic and social impacts (section 131.10(g)(6)). In such cases, the 

limiting factor specifies the highest attainable effluent condition, meaning that performing an analysis of 

what is not feasible to attain (i.e., the levels of pollutant control that caused substantial and widespread 

economic and social impacts) informs the state’s or authorized tribe’s determination of HAC for the 

duration of the WQS variance. Although EPA agrees that monitoring and assessing the receiving waters 

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can be important to evaluate progress toward the underlying designated use, the CWA does not require 

states and authorized tribes to conduct ambient monitoring. To the extent states and authorized tribes 

conduct monitoring, the public can use that information to compare the current ambient condition of 

the receiving waters with the criteria of the underlying designated use and determine “how much the 

variance varies from existing EPA-approved scientifically-based water quality standards” without the 

need to estimate the difference in advance. EPA believes that requiring identification of both a 

quantifiable criterion and quantifiable effluent condition is unnecessary and could potentially hinder the 

use of WQS variances to make water quality progress.

Commenters say that identification of both a numeric criterion and numeric effluent condition is 

necessary to protect existing uses. These commenters do not explain why both a numeric criterion and 

numeric effluent condition is necessary to protect existing uses. For more discussion on protection of 

existing uses and WQS variances, see response Essay 8f. Furthermore, the final rule does not distinguish 

between different types of uses with regard to the applicability of WQS variances. The final rule provides 

WQS variances for the purpose of making water quality progress when the underlying use is not 

attainable in the near term. It is important to provide a mechanism to make water quality progress 

toward the underlying use regardless of the type of use. 

T. EPA Should Require a Pollutant Minimization Program for Every Water 

Quality Standards Variance

EPA agrees that a PMP may often be relevant where a WQS variance is justified, and states and 

authorized tribes should, as a general matter, consider a PMP when identifying the HAC for any WQS 

variance. In fact, EPA specifically included language in the final rule at section 131.14(b)(2)(ii) to highlight 

PMPs in a state’s or authorized tribe’s description of the pollutant control activities that the state or 

authorized tribe anticipates implementing throughout the WQS variance term to achieve the HAC. 

However, EPA cannot determine in advance all possible circumstances where a PMP may be appropriate

and therefore concluded it is not appropriate to require a PMP for all WQS variances. EPA recognizes the 

possibility that there may be circumstances where a PMP is not appropriate or even possible. EPA 

believes preamble and regulatory text of the final rule provides sufficient requirements and guidance to 

ensure that states and authorized tribes include a PMP in a WQS variance when appropriate, and that 

including such a requirement in the final rule is unnecessary and overly prescriptive. Furthermore, WQS 

variances must be reviewed and approved or disapproved by EPA on a case-by-case basis. EPA believes 

such oversight authority will ensure that WQS variances will appropriately reflect the HAC as required by 

the final rule.

U. Water Quality Standards That Apply during a Variance

EPA disagrees with commenters who said EPA should remove language regarding WQS variance 

limitations to 402 permitting and 401 certification in section 131.14(b)(1)(ii) of the proposed rule for the 

reasons they provided (as discussed below). However, EPA notes that the Agency restructured the 

submission requirements section based on other comments and the language these commenters refer 

to no longer exists in the submission requirements section. Some commenters suggest deletion based 

on their overall concern that WQS variances should be at state discretion and only variance policies 

should be reviewed and approved by EPA. For a response to the issue regarding whether or not WQS 

variances, themselves, are WQS that need EPA review and approval, see response Essay 8.f.i.

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Another commenter suggested the deletion of that same language because they believe it conflicts with 

the requirements of CWA section 303(c)(3). For a response regarding this commenter’s concern about 

EPA “utilizing a bifurcated approach for implementing WQS” see response Essay 8.f.i. The commenter 

should also refer to response to 8.g.i for a response to their other suggested deletion to the “Submission 

Requirements” section. 

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Essay 8.g.iii – Variances Submission Requirements: Expiration Dates 

In the preamble to the proposed rule, the U.S. Environmental Protection Agency (EPA) referred to the 

“expiration” date for water quality standards (WQS) variances. This term created concern and confusion 

among some commenters that upon expiration, WQS variances could not be renewed or reissued. EPA’s 

proposed ten-year maximum term was interpreted by these commenters to mean that a WQS variance 

would never exceed ten years, including that the WQS variance could not be renewed or reissued. This 

was not EPA’s intention. EPA never intended that WQS variances could not be renewed or reissued if 

justified under the new regulation. While the final rule does remove the ten-year maximum term, the 

final rule still requires that all WQS variances must have a term limit, based on the required justification, 

upon which the WQS variance ends (or expires) unless it is renewed or reissued in compliance with the 

final regulations.

A. Maximum Term

Several commenters said that a 10-year maximum term is too long for the term of a variance because 

variances should be for only short periods of time for very limited situations. Commenters suggested 

alternatives to a ten-year maximum term such as five years or three years. Commenters said that a 

maximum WQS variance term of five years is more appropriate because five years represents one 

permit cycle, and requiring evaluation of a WQS variance at permit re-issuance would be 

administratively efficient. Commenters also said that a five year maximum term is more appropriate

because the “Water Quality Guidance for the Great Lakes System” (i.e., Great Lakes Initiative [GLI]) 

provides for a maximum WQS variance term of five years, and EPA cites to the GLI in the preamble of 

the proposed rule as an example of how regulatory provisions for WQS variances encourage their 

appropriate utilization (60 FR 15366, March 23, 1995; Title 40 of the Code of Federal Regulations (CFR) 

Part 132). Commenters suggested a maximum WQS variance term of three years because three years 

represents one triennial review cycle during which states and authorized tribes are already required to 

review their WQS. Commenters suggested a maximum WQS variance term of six years because six years 

represents two triennial review cycles, and also accommodates one National Pollutant Discharge 

Elimination System (NPDES) permit cycle plus one year to accommodate administrative delays in reissuing the permit. Commenters said that EPA should include an administrative continuance mechanism 

in section 131.14 to clearly provide that WQS variances will continue past any expiration period as long 

as the regulated entity submits a timely renewal application. Commenters also suggested different 

combinations of a maximum WQS variance term and maximum number of permissible WQS variance 

renewals.

Commenters said that the proposed ten-year maximum duration of a WQS variance was too long 

because the rule did not contain sufficient safeguards to ensure that the highest attainable condition 

(HAC) identified in the WQS variance is, in fact, the HAC, and shorter duration WQS variances were 

needed to ensure a timely reevaluation. Commenters also said the proposed rule did not adequately 

ensure states and authorized tribes would incorporate better than expected water quality 

improvements into the implementing NPDES permits, and shorter duration WQS variances would ensure 

the permitting authority had the opportunity to do so. Commenters also said that the proposed rule will

result in delayed or unrealized water quality improvements because it lacks accountability, and 

suggested that shorter duration WQS variances would provide more accountability. These comments 

suggested a strong desire for more accountability in the final rule to ensure that WQS variances are used 

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appropriately. Although EPA agrees that states and authorized tribes must be held accountable for 

utilizing WQS variances appropriately, EPA disagrees with these commenters that the best way to do it is 

by shortening the maximum term of a WQS variance (see below).

Another group of commenters said that the proposed 10-year maximum WQS variance term would

result in unnecessary rulemaking burden, discourage the use of WQS variances, and impede progress 

toward achieving designated uses. Many states use conventional rulemaking processes to fulfill the 

requirement that any WQS must be a binding provision adopted or established pursuant to state or 

tribal law. Because a WQS variance is itself a WQS, many states and authorized tribes would need to 

adopt a WQS variance through the conventional rulemaking process that states identified as slow and 

administratively burdensome. Many commenters characterized the proposed 10-year maximum as an 

arbitrary time period unrelated to the water quality challenge the state or authorized tribe may be 

trying to address. These commenters stated that the 10-year maximum term would create unnecessary 

state or tribal rulemaking burden by requiring renewal of a WQS variance that may be initially justifiable 

for more than 10 years. 

Commenters expressing concern about rulemaking burden and unrealistic expectations associated with 

an expiration date and maximum 10-year WQS variance term suggested that EPA lengthen or eliminate 

the maximum term of a WQS variance. These commenters suggested that doing so would result in 

achieving the same environmental benefits, while reducing rulemaking burden. Commenters suggested 

alternatives such as increasing the maximum term of a WQS variance to 14 years to reflect the NPDES 

permit cycle, plus allowing for administrative delays in reissuing the permit. Alternatively, commenters 

suggested that, rather than specify a maximum WQS variance term, EPA should require that a WQS 

variance must be “as short as possible” and allow the state or authorized tribe to determine the 

appropriate term similar to how states and authorized tribes establish permit compliance schedules

(CS). Some commenters suggested that if EPA were to eliminate the maximum variance term, EPA could 

require states and tribes to conduct “interim reviews at regular intervals.” 

EPA carefully considered all of the comments. EPA decided that the use of WQS variances would work 

best if the rule did not impose a set ten-year maximum timeframe. EPA agreed with the comments that 

identified concerns with setting one maximum timeframe that would apply to all WQS variances. The 

proposed maximum ten-year timeframe would impose additional regulatory burdens for reissuance of 

WQS variances in situations where it could be demonstrated at the time of WQS variance issuance that 

more than ten years could be justified. Also, EPA decided that having the ten-year maximum term may 

have an unintended consequence of implying that ten years could be the default term for a WQS 

variance. That was not EPA’s intent and the final rule requires WQS variances to have a term that is only 

as long as necessary and the term must be justified. So while EPA decided not to include a maximum 

ten-year term limit in the final rule, the final rule does require that every variance have a term upon 

which the WQS variance will expire (section 131.14(b)(1)(iv)). EPA also concluded that the commenters 

generally were either concerned that the proposed rule did not provide sufficient regulatory safeguards 

to ensure that WQS variances are used appropriately, or will result in an unnecessary rulemaking 

burden, discourage the use of WQS variances, and impede progress toward achieving designated uses. 

To address both of these concerns in the final rule, EPA made select revisions in the final rule to

maximize accountability and minimize state and tribal burden.

To minimize state and tribal rulemaking burden, EPA removed the requirement that any WQS variance 

have a maximum term of ten years. Without a maximum ten-year variance term, the rule provides 

states and authorized tribes with the flexibility to establish the term of the WQS variance that is 

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appropriate and justified for each WQS variance. The final rule further reduces burden by providing

greater flexibility in the way states and authorized tribes can articulate the HAC. In particular, the final 

rule provides states and authorized tribes the option, for discharger-specific WQS variances, of 

articulating the HAC as only an interim criterion or as an interim effluent condition that reflects the 

greatest pollutant reduction achievable. These provisions will ensure that the final rule provides the 

needed flexibility states and authorized tribes need to utilize WQS variances for the purpose of making

progress toward achieving designated uses that are not immediately attainable but may be attainable in 

the future. Finally, the final rule includes a requirement for WQS variances with a duration greater than 

5 years to automatically incorporate the HAC that is identified during a reevaluation of the WQS 

variance, which eliminates the need for an additional WQS rulemaking. 

To balance greater flexibility provided by elimination of a maximum variance term, the final rule 

includes several provisions to ensure state and authorized tribal accountability for utilizing WQS 

variances appropriately. First, the final rule requires states and authorized tribes to justify the term of 

any WQS variance by including in the documentation submitted to EPA for review and approval or 

disapproval, a description of the pollutant control activities that are expected to occur during the WQS 

variance term to achieve the HAC and make progress toward meeting the underlying designated use and 

criteria. This provision will help ensure that each WQS standard is as short as possible, and addresses 

the concern by some commenters of a “default” term length dictated by a regulatory maximum term.

Second, for any WQS variance with a duration greater than 5 years, the final rule requires a state or 

authorized tribe to adopt into state or tribal regulation a schedule to reevaluate a WQS variance (with 

public input) no less frequently than every five years after EPA approves the WQS variance, and to 

submit the results of the reevaluation to EPA within 30 days of completion. EPA determined that 

requiring a reevaluation every five years will ensure that the state or authorized tribe and public assess 

updated information and changed circumstances to determine whether continuation of the WQS 

variance continues to be justified. The results of the reevaluation must be submitted to EPA, allowing 

EPA to carry out its oversight role. To ensure that states and authorized tribes reevaluate the WQS 

variance according to the schedule they have adopted, the final rule also requires a WQS variance to 

include a provision that specifies the WQS variance will cease to be the applicable WQS for Clean Water 

Act (CWA) purposes if the state or authorized tribe does not reevaluate the WQS variance on the 

specified schedule or does not submit the results to EPA within 30 days of completion. Finally, to ensure 

that a state or authorized tribe utilizes the results of a WQS variance reevaluation to make water quality 

progress throughout the WQS variance term, the final rule requires states and authorized tribes to 

specify in the WQS variance that the HAC applicable during the WQS variance term shall be either the 

HAC identified at the time the initial WQS variance was adopted, or the HAC later identified during any

required reevaluation, whichever is more stringent. These provisions will help ensure “prompt action to 

address nonattainment.” EPA determined that the combination of these refinements to the final rule 

removed the need for a maximum term of a WQS variance in the rule and addressed the concerns of 

commenters for achieving the desired environmental benefits from WQS variances.

The EPA concludes that all together, the provisions in section 131.14 of the final rule provide states and 

authorized tribes with the flexibility they need to utilize WQS variances effectively, while providing the 

public with the transparency and regulatory structure needed to ensure that WQS variances are utilized 

appropriately. 

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B. Water Quality Standards Variances Should Not Let Dischargers Continue in 

Status Quo

EPA agrees with commenters that said a WQS variance “should not be used to allow permanent 

dischargers that negatively impact the quality of waters of the US,” allow dischargers to continue “the 

status quo,” or allow a WQS variance to become “the acceptable norm.” EPA’s position is that provisions 

in the final rule address the concerns of the commenters.

The final rule includes several provisions to ensure that the requirements of a WQS variance are met as 

quickly as possible and that the result of a WQS variance is as much water quality progress as possible. 

As described above, the final rule requires states and authorized tribes to provide to EPA, 

documentation that the term of the WQS variance is only as long as necessary to achieve the HAC, and 

that such documentation must justify the term of the WQS variance by describing the activities and 

milestones that will occur during the WQS variance term (see section 131.14(b)(2)(ii)). In cases where a 

WQS variance requires the performance of certain studies, the state or authorized tribe must justify the 

term of the WQS variance in the context of the time required to perform those studies (as well as any 

other requirements of the WQS variance). The final rule requires states and authorized tribes to 

reevaluate a WQS variance longer than five years at least every five years, and submit the results of such 

reevaluations to EPA within 30 days. The final rule also requires states and authorized tribes to include 

in the WQS variance a provision that the WQS variance will no longer apply if the state or authorized 

tribe does not perform the reevaluations on the specified schedule or does not submit the results to EPA 

within 30 days. Additionally, the final rule requires states and authorized tribes to include a provision in 

the WQS variance that specifies the requirements of the WQS variance as reflecting either the HAC

identified at the time of the adoption of the WQS variance, or the HAC later identified during any 

reevaluation, whichever is more stringent. Finally, the final rule requires states and authorized tribes to

include all limitations and requirements necessary to implement the WQS variance as enforceable 

conditions of the NPDES permit for the permittee(s) subject to the WQS variance. EPA believes these 

provisions in the final rule will ensure that the requirements of a WQS variance are utilized 

appropriately and will not lead to dischargers receiving variances that allow dischargers to continue to 

operate under the “status quo” when a better condition is attainable (which the Agency thinks should 

almost always be the case either through improved treatment or implementation of pollutant 

minimization programs [PMPs]). 

C. Renewals

Commenters expressed confusion about the proposed rule’s requirements for an expiration date and 

what it meant for adopting a subsequent WQS variance. Commenters said: “The proposed rule at 

§ 131.14(b)(1)(iii) proposed that the state or authorized tribe specify the ‘date the WQS variance will 

expire’ and required that the expiration date must be ‘as short as possible, but expire no later than 

10 years...’” These comments suggest that commenters thought the proposed rule at 

section 131.14(b)(1)(iii) only allowed a permittee one WQS variance for a total of 10 years, and that 

renewal of the WQS variance beyond a total of 10 years would not be allowed. These commenters said

that many water quality challenges would require more than 10 years to address, and that limiting a 

WQS variance to 10 years in total for any particular permittee would be insufficient.

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EPA does not intend to limit states and authorized tribes to a single WQS variance term. EPA clarifies in 

the final rule that a state or tribe may adopt a subsequent WQS variance to replace a WQS variance that 

has or will expire provided that the new WQS variance satisfies all the requirements of section 131.14

(see section 131.14(b)(1)(iv)). 

D. Best Management Practices 

Commenters said that EPA “requires documentation for any subsequent renewals that includes 

‘whether and to what extent BMPs have been implemented to address the pollutant(s) subject to the 

water quality standard (WQS) variance and the water quality progress achieved during the WQS 

variance period.’ This will establish a significant burden on permittees ... to generate proof for a 

regulatory standard that is not adequately defined and likely to be interpreted inconsistently across EPA 

regions. The likely outcome is increased costs for engineering and scientific studies, regulatory 

negotiations, and potential litigation.” The final rule only requires identification and documentation of 

any cost-effective and reasonable best management practices (BMPs) for nonpoint sources (NPS)

related to the pollutant(s) and location(s) specified in the WQS variance that could be implemented for a

water body to make progress towards attaining the designated use and criterion for a WQS variance 

applicable to a water body or waterbody segment (one not limited to a specific discharger or 

dischargers). Such a requirement is not applicable to individual permittees such as described by the 

commenter. See comment response topic 8.g.v for additional information on requirements related to 

cost-effective and reasonable BMPs for NPS. 

E. Variance Review at the End of the Water Quality Standards Variance Term

Commenters said: “We are not certain why two reviews – during the triennial review and again at the 

end of the variance term - are necessary” or “We support stating that variances do not need to be 

evaluated at each triennial review and that variance reviews would only take place upon renewal of the 

applicable NPDES permit.” The final rule does not require a review of the WQS variance at the end of the 

WQS variance term. The commenters may have misinterpreted the proposed rule’s requirement that 

“the state or tribe must meet the requirements of § 131.14 and provide appropriate documentation of 

the steps taken to meet the requirements of the previous variance” as a requirement to review all WQS 

variances at the end of the WQS variance term. EPA’s intention is to require the state or authorized tribe 

to submit sufficient documentation to allow EPA to review a subsequent renewal or reissuance of a 

WQS variance in the context of the water quality progress that was made during the previous WQS 

term. See also the discussions in subsection F and G of this essay which pertain to coordination of the 

reevaluations and triennial reviews and/or permit renewal.

F. Relationship between the Term of Water Quality Standards Variance and 

the Five-Year Term of a National Pollutant Discharge Elimination System

Permit

Commenters said that EPA should clarify how the term of a WQS variance and the term of the 

implementing NPDES permit will work together. One example given was when “a variance expires 

before the permit expires.” Commenters also said EPA should clarify that interim permit limits and other 

variance conditions continue to apply until such time as a variance or permit is renewed. Commenters 

questioned if a “variance must be as short as possible...” means that EPA could require WQS variances to 

last less than one permit term, and suggested that such a requirement “could cause issues with the 

permit backlog by creating the need to modify and reissue permits mid-term.” The final rule specifies 

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that the term of a WQS variance must be only as long as necessary to achieve the HAC. For a response to 

these and other comments on the coordination of NPDES permits and the term of a WQS variance, 

including comments on administratively continued permits, see EPA’s response essay for code 8.f.ii.

Commenters also recommended EPA clarify the rule to state that the ten-year term commences to run 

upon issuance of the permit or permits implementing the variance because state regulatory processes 

to approve a variance policy and to issue permits implementing the variance can each be very lengthy.

The final rule does not specify a maximum WQS variance term. As such, EPA does not envision there 

being a problem with synchronizing efforts to improve water quality (as may be required in a permit) 

and the term of the variance.

G. Triennial Reviews of Water Quality Standards Variances

Commenters said that a WQS variance should not need to be reviewed as part of the triennial review 

process. Commenters also interpreted the proposed rule to specify that the WQS variance review 

process is to be reviewed on a triennial basis rather than a triennial review of individual variances, and 

that clarification is necessary. EPA disagrees with these comments. A WQS variance is a WQS subject to 

the same review and public participation requirements specified in section 131.20 as any other WQS.

Although a WQS variance is subject to the review and public participation requirements specified in 

section 131.20, traditionally, reevaluation of WQS variances during triennial reviews may not have 

always received the attention they warranted. 

Therefore, separate and apart from the traditional triennial review process, the final rule includes 

requirements for reevaluation of WQS variances with terms longer than five years. In practice, many 

states and authorized tribes that currently utilize WQS variances actively reevaluate WQS variances in 

association with their expiration and renewal. Such a mechanism may be sufficient for a WQS variance 

with a relative short duration (e.g., less than 5 years), however, the public could not reasonably expect 

expiration and renewal to properly function as a reevaluation mechanism for a WQS variance with a 

long duration. As an alternative to the proposed ten-year maximum WQS variance term, the final rule 

eliminated any maximum term and instead requires states and authorized tribes to reevaluate all WQS 

variances (with terms greater than 5 years) at least every five years. EPA expects states and authorized 

tribes to proactively search for new or updated data and information during each WQS variance 

reevaluation and allow for public involvement. New or updated data and information includes but is not 

limited to new information on pollutant control technologies, changes in pollutant sources, flow or 

water levels, economic conditions, and BMPs that impact the HAC or the time needed for the WQS 

variance.

To provide sufficient assurance that a state or authorized tribe would actively reevaluate a WQS 

variance at a reasonable and predictable interval, the final rule includes the requirements that a state or 

authorized tribe include a schedule of reevaluations that must begin within 5 years of the EPA’s approval 

and occur no less frequently than every five years, specify how the state or authorized tribe intends to 

obtain public input on the reevaluations, submit the results of the reevaluations to the EPA within 30 

days of the completion, and include a provision in the WQS variance that states the WQS variance will 

cease to be the applicable WQS for CWA purposes if the state or authorized tribe does not conduct the 

reevaluation on the specified schedule or does not submit the results of the reevaluation to the EPA 

within 30 days of completion. The EPA chose five years as the maximum interval between reevaluations 

because five years is a single permit cycle, and a state or tribe can use the flexibility in the provision to 

synchronize the reevaluation schedule with the NPDES permit reissuance process or with their triennial 

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reviews. The EPA notes that specifying five years as the maximum interval between reevaluations does 

not preclude a state or authorized tribe from requiring reevaluation of a WQS variance at shorter 

intervals if deemed appropriate. However, the final rule requires that states and authorized tribes 

include a provision in the WQS variance that the WQS variance will no longer be the applicable WQS for 

CWA purposes if the state or authorized tribe does not conduct the reevaluation consistent with the 

scheduled specified in the WQS variance or if the results are not submitted to EPA as required (section 

131.14(b)(1)(vi)).

Although a state or authorized tribe may choose to reevaluate a WQS variance during the triennial 

review, the EPA recognizes that many states and authorized tribes prioritize their triennial review of 

standards and are more likely to critically evaluate a WQS variance in association with reissuance of the 

implementing NPDES permit. It is important to note that WQS variance reevaluations on a five-year 

permit cycle would not replace the requirement to conduct triennial reviews. If the state or authorized 

tribe chooses to link the WQS variance reevaluation to its NPDES permitting process, the state or 

authorized tribe must nevertheless consider the WQS variance during the state WQS triennial review, 

even if a WQS variance term is shorter than 5 years. The EPA notes that it does not take action to review 

and approve or disapprove the results of a WQS variance reevaluation under CWA section 303(c)(4)(A). 

However, the results of the reevaluation will be important to ensure that re-issued permits continue to 

derive from and comply with applicable WQS and could inform an Administrator’s Determination under 

CWA section 303(c)(4)(B). 

H. General Support

EPA acknowledges comments supporting the proposed rule.

I. How to Articulate the Term of the Variance

Commenters suggested that EPA allow alternative ways to express the term of a WQS variance and 

opposed the rule’s specific ten-year maximum term. The final rule requires states and authorized tribes 

to include a definite term for the WQS variance (at which time the variance either ends or must be 

renewed or reissued), but no longer includes the ten-year maximum term. The final rule also allows 

states and authorized tribes to articulate the term of a WQS variance that is as short as possible and is 

consistent with the demonstration provided in section 131.14(b)(2) by either specifying an interval of 

time with respect to EPA-approval of the WQS variance, or a specific date. 

J. Should Not Prohibit Modifications to a Water Quality Standards Variance 

before It Expires

Commenters said that nothing in the final rule or preamble to the final rule should prohibit a state’s 

authority to adopt revisions to a WQS variance, or to replace any provision of a WQS variance prior to its 

expiration date. EPA agrees with this comment. Nothing in the final rule or preamble to the final rule 

prohibits a states and authorized tribes from adopting revisions to a WQS variance, or to replace any 

provision of a WQS variance prior to its expiration date provided that the revisions are consistent with 

all the provisions of section 131.14. Similar to the WQS variance itself, revisions to a WQS variance is a 

revision to a WQS subject to public participation requirements and EPA review and approval or 

disapproval.

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K. Performance-Based Approach

Commenters said that WQS variances should have performance-based requirements, not a prescriptive 

time limit as all WQS variances do not fit into a single category. EPA does not agree that performancebased requirements should be adopted for variances. As described in “EPA Review and Approval of State 

and Tribal Water Quality Standards,” 65 FR 24641-24653, April 27, 2000, the ‘‘performance-based’’

approach may be suited for deriving site-specific numeric criteria and for interpreting narrative criteria 

into quantifiable measures because it can result in consistent application of State and Tribal narrative 

water quality criteria and defensible site-specific adjustments to numeric ambient water quality criteria. 

Site specific translations of narrative water quality criteria and site specific adjustments to numeric 

ambient water quality criteria take additional information into account while protecting the designated 

use. As such the intended level of protection is no way modified. Changes to designated uses and WQS 

variances, however, do not lend themselves to a ‘‘performance-based’’ approach because criteria 

changes modify the intended level of protection. In addition, making use changes and issuing variances

for CWA section 101(a)(2) uses must include an evaluation of ‘‘attainability’’ of a designated use, taking 

into account factors such as natural conditions or economic and social impacts. See Title 40 of the Code 

of Federal Regulations (CFR) section 131.10(g) for the attainability factors. 

L. Ten-year Maximum Expiration Date Is Unnecessary

Commenters said that requiring expiration of WQS variances no later than 10 years after state adoption 

is unnecessary because “any variance must be renewed as a part of the state triennial review process.” 

The final rule does not require renewal of a WQS variance as part of the state triennial review process.

In addition, the final rule does not require a maximum WQS variance term of ten years. States and 

authorized tribes must specify the term of a WQS variance and justify the term. The final rule requires 

reevaluation of a WQS variance with a term longer than five years at least every five years. Requiring 

reevaluation at least every 5 years will ensure that WQS variances are utilized appropriately. For WQS 

variances that are up for renewal at the time of a state’s or authorized tribe’s triennial review, the final 

rule does not prohibit utilizing the triennial review and related rulemaking process for adoption of 

revised WQS variances.

Commenters suggested that “a variance could remain in effect until a State makes a determination that 

the WQS is attainable, through a UAA.” This is contrary to EPA’s long established position that WQS 

variances are time-limited. This continues to be EPA’s position and the final rule includes, at 

section 131.3(o), a definition of a WQS variance as “a time-limited designated use and 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 without a term limit essentially could become a 

permanent change to the designated use and criterion, and does not achieve EPA’s objective of 

providing a mechanism to allow states and authorized tribes to make water quality progress, and ensure 

such progress is made, when the underlying designated use is not immediately attainable.

M. EPA Should Require a Water Quality Standards Variance to Be Re-Justified 

at Least Every Three Years

Commenters said EPA should require States “to review any variance at least every three years as 

mandated by Section 303(c) for all water quality standards, and which is consistent with the 

longstanding EPA requirement that ‘the variance is granted for a specific period of time and must be rejustified upon expiration but at least every 3 years (Note: the 3-year limit is derived from the triennial 

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review requirements of section 303(c) of the Act.)’” EPA agrees that states and authorized tribes should 

be required to review a WQS variance at least every three years. However, EPA disagrees that states and 

authorized tribes should be required to re-justify a WQS variance at least every three years.

A WQS variance is a new or revised WQS subject to EPA review and approval or disapproval, requires a 

public process, and must be reviewed on a triennial basis. The triennial review requirement applicable 

to a WQS variance is the same for any WQS: CWA section 303(c)(1) requires states and tribes to hold 

public hearings at least once every 3 years for the purpose of reviewing applicable WQS and, as 

appropriate, modifying and adopting standards. However, the Act does not explicitly require “rejustification” of each and every WQS. In the same way the Act does not require re-justification of every 

WQS, the final rule does not require re-justification of every adopted WQS variance at each triennial 

review. See additional discussion under subsection G of this essay. 

In addition to the traditional triennial review, the final rule requires states and authorized tribes to

reevaluate WQS variances on a regular and predictable schedule. EPA’s position is that the reevaluation 

requirements in the final rule are sufficient to address the need for evaluating long-term WQS variances 

on a periodic basis. EPA does not agree with the commenters who suggested a reevaluation and rejustification every three years. EPA’s final rule requires a re-justification if the state or authorized tribe 

decides to renew or reissue the WQS variance.

As described in other subsections of this essay, to ensure that a WQS variance reflects the HAC

throughout the WQS variance term, the final rule requires states and authorized tribes to adopt a 

provision specifying that the applicable interim WQS shall be either the HAC initially adopted, or a higher 

attainable condition later identified during any reevaluation for WQS variances longer than five years. 

This provision is required to be self-implementing so that if any reevaluation yields a more stringent 

attainable condition, that condition becomes the applicable interim WQS without additional action. 

Upon permit reissuance, the permitting authority will base the water quality-based effluent limit 

(WQBEL) (and permit terms and conditions) on the more stringent interim WQS consistent with the 

NPDES permit regulation at section 122.44(d)(vii)(A). Where the reevaluation identifies a condition less 

stringent than the HAC, the state or authorized tribe must revise the WQS variance consistent with CWA 

requirements and obtain EPA approval of the WQS variance before the permitting authority can derive a 

WQBEL based on that newly identified HAC. 

In addition, the final rule requires states and authorized tribes to specify, in the WQS variance, the 

reevaluation frequency and how they plan to obtain public input on the reevaluation, and they must 

submit the results of the reevaluation to EPA within 30 days of completion. States and authorized tribes 

may specify the frequency of reevaluations to coincide with other state and authorized tribal processes 

(e.g., WQS triennial reviews or NPDES permit reissuance), as long as reevaluations occur at least every 

five years. Although EPA does not review and approve or disapprove the results of a WQS variance 

reevaluation, the results could inform whether the Administrator exercises his or her discretion to 

determine that new or revised WQS are necessary. The rule also requires states and authorized tribes to 

adopt a provision specifying that the WQS variance will no longer be the applicable WQS for CWA 

purposes if they do not conduct the required reevaluation (including public input) or do not submit the 

results of the reevaluation within 30 days of completion. EPA determined that this provision was the 

most effective way to ensure that the state or authorized tribe conducts the important and necessary 

five-year reevaluation evaluation and provides the results of their review to EPA. In the absence of a 

state or tribal reevaluation, EPA concluded that the WQS variance should not continue. Rather than 

requiring a separate state action or EPA action, the final rule requires the initial state or tribal WQS 

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variance submission to include such a provision. If a state or authorized tribe does not reevaluate the 

WQS variance or does not submit the results to EPA within 30 days, the underlying designated use and 

criterion become the applicable WQS for the permittee(s) or water body specified in the WQS variance 

without EPA, states or authorized tribes taking an additional WQS action. In such cases, subsequent 

NPDES WQBELs for the associated permit must be based on the underlying designated use and criterion 

rather than the HAC, even if the originally specified WQS variance term has not expired.

EPA initially proposed a maximum allowable WQS variance term of 10 years to ensure that states and 

authorized tribes reevaluate long-term WQS challenges at least every 10 years before deciding whether 

to continue with a WQS variance. EPA explained in the preamble to the proposed rule that the purpose 

of this maximum WQS variance term was as follows: “Establishing an expiration date will ensure that the 

conditions of a [WQS] variance will be thoroughly reevaluated and subject to a public review on a 

regular and predictable basis to determine (1) whether conditions have changed such that the 

designated use and criterion are now attainable; (2) whether new or additional information has become 

available to indicate that the designated use and criterion are not attainable in the future (i.e., data or 

information supports a use change/refinement); or (3) whether feasible progress is being made toward 

the designated use and criterion and that additional time is needed to make further progress (i.e., 

whether a [WQS] variance may be renewed).” 

Some commenters suggested that 10 years is too long and does not provide adequate assurance that 

the state or authorized tribe will periodically reevaluate a WQS variance in a publicly transparent 

manner. Other commenters suggested that 10 years is too short because states often adopt WQS 

variances through conventional rulemaking processes and that such a maximum term would result in 

unnecessary rulemaking burden where it is widely understood that long-term pollution challenges 

require more time to resolve. A 10-year maximum could also discourage the use of WQS variances. In 

response, EPA concluded that establishing specific reevaluation requirements for WQS variances longer 

than five years is the best way to achieve EPA’s policy objective of active, thorough, and transparent

reevaluation by states and authorized tribes while minimizing rulemaking burden. The reevaluation 

requirements in the rule eliminate the need to specify a maximum WQS variance term because they 

ensure the HAC is always the applicable WQS throughout the WQS variance term, thus driving 

incremental improvements toward the underlying designated use. These requirements also ensure the 

public has an opportunity to provide input throughout the WQS variance term. EPA chose five years as 

the maximum interval between reevaluations because five years is the length of a single NPDES permit 

cycle, allowing the reevaluation to inform the permit reissuance process. Although the rule does not 

specify a maximum WQS variance term, states and authorized tribes must still identify the WQS variance 

term and provide documentation demonstrating that the term is only as long as necessary to achieve 

the HAC. EPA will use this information to determine whether to approve or disapprove the WQS 

variance submitted for review, based on the requirements in section 131.14.

N. The Rule Should Allow EPA to Modify the Term (Expiration Date) of the 

Variance

Commenters said that the final rule should provide that “EPA reserves the right to modify the expiration 

date of the variance in the event that the state fails to demonstrate that the full timeframe requested is 

necessary.” These commenters are concerned that a WQS variance for a term longer than necessary will 

“discourage prompt action to address non-attainment” of WQS. EPA agrees that states and authorized 

tribes must demonstrate the full timeframe of a WQS is necessary. However, EPA disagrees with the 

commenter’s proposed method for achieving this outcome.

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The final rule at section 131.14(b)(iv) specifies that the term of the WQS variance must only be as long 

as necessary to achieve the HAC 131.14(b)(iv). To ensure EPA has sufficient information to determine 

whether the WQS variance is consistent with EPA’s WQS regulation, states and authorized tribes must 

provide documentation to justify why the WQS variance is needed. States and authorized tribes must 

submit all WQS variances to EPA for review and approval or disapproval. If the state or authorized tribe 

does not adequately document the term of the WQS variance, EPA may disapprove the WQS variance.

This is the more appropriate action that EPA attempting to modify a state or tribal submission. The state 

or authorized tribe can decide whether it wants to change its submission to address EPA’s disapproval.

As discussed previously, the final rule includes several provisions (e.g., reevaluation, submittal of 

reevaluation results, inclusion of any more stringent HAC identified during the reevaluation) that 

provide a framework for ensuring progress continues toward the designated use and criterion, even if 

the HAC identified in the WQS variance is achieved before then end of the WQS variance term.

O. Specific Questions

Comment stated: “WDNR requests clarification regarding the time period of the variance. Currently, in 

Wisconsin, variances are granted for the duration of a 5-year permit term, however circumstances 

sometimes delay the reissuance of a permit and its corresponding variance. It is Wisconsin’s 

understanding that variances can only be granted for the length of one permit term. Four elements need 

to be addressed in this definition to make it clear:

1) How many years is a single variance designed to cover?

2) What happens if there is a reissuance delay—can the variance be extended to cover that reissuance 

delay?

3) Can the variance be reissued, and if so, is there a maximum number of reissuances?

4) Is there an absolute timeline for the endpoint of a variance before a facility must achieve their WQBEL 

and will no longer be considered for a reissued variance (i.e., a cap on the total number of variance years)? 

For example: Does this statement mean that a single 10-year variance will be granted to cover two 

permit terms at once? If so, can the 10-year variance be approved for a second 10 years? Is it the EPA’s 

intent to continue to grant variances that extend for the length of the 5-year permit term, including any 

reissuance delay beyond 5 years, but no more than 10 years rather than assigning a specific end date? 

(i.e., if the permit is not reissued until year 8, the single variance would cover it. However, what happens 

if the permit is not reissued until year 11?) Or does this statement mean that variances will be given an 

absolute expiration date of 10 years from the first variance issuance (i.e. no more than one reissuance of 

a 5 year variance before the permittee must meet the WQBEL)?” 

The commenter asked a series of implementation questions, not specific comments requesting revisions 

to the proposed rule. EPA intends to issue implementation guidance which should address the questions 

raised by the commenter. Nevertheless, EPA provides the following responses to some of the 

commenters’ questions. The clarifications the commenter requested are based on the “understanding 

that variances can only be granted for the length of one permit term.” The final rule does not restrict

states and authorized tribes to any specific WQS variance term. The final rule specifies that if, at the end 

of the variance, the underlying designated use remains unattainable, the state or authorized tribe may 

adopt a subsequent WQS variance(s), consistent with the requirements of section 131.14.

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The preamble of the final rule addresses many of the commenter’s questions about what happens if a 

state or authorized tribe does not coordinate a WQS variance term with the expiration date of an NPDES 

permit. The preamble of the final rule also addresses how the final rule affects states and authorized 

tribes under the 1995 Great Lakes Water Quality Guidance (GLWQG) because those requirements are 

different than the WQS variance requirements in final rule. For waters in the Great Lakes basin, states 

and authorized tribes must meet the requirements of both 40 CFR Parts 131 and 132. The practical 

effect of this requirement is that, where regulations in 40 CFR Parts 131 and 132 overlap, the more 

stringent regulation applies. In some cases, the flexibilities and requirements in the national rule will not 

be applicable to waters in the Great Lakes basin. For example, the GLWQG limits any WQS variance to a 

maximum term of five years (with the ability to obtain a subsequent WQS variance). Therefore, any 

WQS variance on waters that are subject to the GLWQG cannot exceed five years even though today’s 

final rule in 40 CFR Part 131 does not specify a maximum term. On the other hand, because GLWQG 

WQS variances cannot exceed five years, the requirements in today’s final rule that pertain to 

conducting reevaluations (for WQS variances greater than five years) are not applicable.

EPA notes that some states and authorized tribes have specific WQS and/or permitting requirements 

that are not appropriate to address in this national rule. However, these states and authorized tribes can 

work individually with EPA to address specific issues on a case-by-case basis. See also EPA’s response 

essay for 8.f.ii for more discussion on coordination of NPDES and WQS variance expiration. Additional 

EPA guidance may also become available after publication of the final rule.

P. Use Attainability Analysis for a Water Quality Standards Variance

Commenters said the rule incorporates the criteria for use attainability analysis (UAA) under section 

131.10(g) to establish a variance. For WQS variances to CWA section 101(a)(2) uses, the final rule at 

section 131.14(b)(2)(i) incorporates the factors in section 131.10(g) along with one additional factor. 

Additionally, the preamble to the final rule discusses the level of “scientific rigor” required for a WQS 

variance as compared to a UAA required for changes to 101(a)(2) uses. In summary, the level of rigor 

required for a WQS variance is no different than for a designated use change. However, the appropriate 

technical and scientific data required to support a designated use change and WQS variance can vary 

depending on the complexity of the specific circumstances. EPA recognizes that the data and analyses 

often needed to support adoption of a WQS variance could be less complex and require less time and 

resources compared to removing a designated use because many WQS variances evaluate only one 

parameter for a single permittee for a limited period of time. The level of effort a state or authorized 

tribe needs to devote to a WQS variance will in large part be determined by the complexity of the water 

quality problem the state or authorized tribe seeks to address. See the preamble of the final rule for 

further discussion of this subject.

Q. Relationship between Water Quality Standards Variance Highest Attainable 

Condition and National Pollutant Discharge Elimination System Permit Water 

Quality-Based Effluent Limits

Commenters said that establishing a WQBEL for an NPDES permittee on the basis of the HAC in a WQS

variance is inconsistent with making water quality progress. EPA disagrees with these commenters. The 

relationship between WQS variances and WQBEL for NPDES permits is extensively discussed in the 

preamble to the final rule. See also EPA’s response essay for code 8.g.ii.

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R. Nonpoint Source Controls

Commenters said the effect of the rule will be “Lulling all pollution sources and the political bodies 

(permitting agencies and state legislatures) into a 10-year belief that water quality standards have been 

suspended.” Commenters also said EPA should establish a maximum WQS variance term less than 10 

years because “making circumstances appear to be more dire should be a goal of EPA’s rules” in order to

pressure states and authorized tribes to do more to reduce NPS. EPA disagrees with these commenters. 

The goal of section 131.14 is to provide a regulatory mechanism for states and authorized tribes to make 

progress in meeting the underlying use and criteria for a water body. In a discharger-specific variance 

(single or multiple dischargers), the WQS variance is implemented by reducing discharges from point 

sources consistent with the approved WQS variance rather than remove the underlying designated use.

EPA notes that in a WQS variance applicable to a water body or waterbody segment, the state or 

authorized tribe and stakeholders (including both point and NPS) are working together to make progress 

toward the underlying WQS. EPA believes that “making circumstances appear to be more dire” 

perversely incentivizes removal of the underlying designated use over incremental water quality

improvement. EPA agrees that it is possible a state or authorized tribe may ultimately find that, in a 

discharger specific variance, after reducing all point sources consistent with the requirements of the 

CWA, the underlying designated use is still not attainable without further reductions in NPS of pollution.

In such cases, the state or authorized tribe should continue to implement other water quality 

management options that include NPS controls or, if the stakeholders are willing participants, could 

contemplate the use of a WQS variance applicable to a water body or waterbody segment. See response 

topic 8.g.v for more discussion about NPS of pollutants. 

S. 401 Permitting and Mixing Zones

A commenter suggested striking out regulatory language in proposed section 131.14(b)(1)(ii) that 

provides for issuing certifications under section 401 of the Act based on a variance. EPA rejects this 

comment because 401 certifications are to be based on applicable WQS. If an NPDES permit effluent 

limit is derived from a WQS based on a WQS variance, a 401 certification should be based on that WQS

(see also EPA’s response to Essay 8.f.ii). The commenter also suggested adding in 131.14(b)(1)(ii)(B)

“including increased pollutant loading allowed by changes in mixing zones.” This final rule does not 

directly address mixing zones so EPA did not make the requested change. State or tribal mixing zone 

policies/regulations would continue to apply. However, as discussed in EPA’s response essay for code 

8.f, WQS variance may not result in any lowering of the currently attained ambient water quality (with 

the single exception for the new attainability factor related to dam removal and restoration). As in the 

proposed rule, the provision includes a single exception for the situation where a WQS variance is 

necessary for restoration activities under section 131.14(b)(2)(i)(A)(2)).

T. Commenter Provides Interpretation of the Proposed Rule

EPA thanks the commenters for describing their interpretation of the proposed rule. Public descriptions, 

interpretations, and perceptions of the proposed rule help EPA improve clarity and ensure the final rule 

accomplishes EPA’s goals and objectives.

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Essay 8.g.iv – Variances Submission Requirements: Supporting 

Documentation Demonstrating Need for Variance

A. The Requirements for a Water Quality Standards Variance Should Be Less 

than the Requirements for a Permanent Use Modification

Commenters said that requiring states and authorized tribes to justify a water quality standards (WQS) 

variance using at least one of the six factors listed in section 131.10(g) “provides the automatic 

assumption that a use attainability analysis is required and the designated use must be removed or 

lowered to the highest attainable use.” Commenters suggested the U.S. Environmental Protection 

Agency (EPA) clarify that the “burden of proof to gain approval for a short term variance should be less 

than for approval of a permanent use modification.” 

The final rule at section131.14 provides the regulatory requirements for WQS variances. For WQS

variances for Clean Water Act (CWA) 101(a)(2) uses, EPA decided that it was most appropriate to include 

the same factors for justifying a WQS variance as appear in section 131.10(g) for downgrading a use. The 

underlying concept behind both a use removal and a WQS variance (a time-limited use and associated 

criteria) is attainability, as in the “wherever attainable” phrase in section 101(a)(2) of the CWA.

Therefore, EPA determined it was appropriate to use the same factors for both regulatory provisions.

The time-limited nature of a WQS variance suggests an additional appropriate factor (restoration 

activities). It is difficult to compare a use removal demonstration with a WQS variance demonstration in 

terms of “burden of proof” or “rigor of analysis” because, although the same factors are the basis for 

justifying a use downgrade or a WQS variance, analyses for the two decisions will be affected by the 

inherent differences between justifying a permanent downgrade and a temporary downgrade. For 

example, a WQS variance may be appropriate when there is compelling evidence of unattainability 

during the period of the WQS variance, but uncertainty in the final outcome of implementing pollutant 

minimization program (PMP) requirements. The type and level of analyses would be determined by the 

factors and time periods to be demonstrated. In contrast, a use removal is more appropriate where 

there is more certainty in characterizing the highest attainable use (HAU) and substantial changes in 

conditions and circumstances are not anticipated. This may be a different type and degree of analysis 

but still based on one or more of the same fundamental factors for justifying a revision to the use. See 

the discussion in the section II.E of the preamble to the final rule which discusses whether there is a 

difference in “rigor” between the two types of analyses.

While the new rule includes the same factors for justifying a WQS variance for a 101(a)(2) use,

requirements in the new rule carefully balance the flexibility states and authorized tribes need to 

effectively utilize WQS variances, with the accountability and transparency the public needs to be 

assured that WQS variances are used appropriately. The “burden of proof” needed to justify a WQS 

variance can vary depending on the complexity of the specific circumstances. Nevertheless, the EPA 

recognizes that the effort needed to support adoption of a WQS variance will often be less than the 

effort needed to support removing a designated use. A use attainability analysis (UAA) needed to 

remove a designated use often requires evaluation of more than one water quality parameter, multiple 

sources of pollutants, and extended time horizons. A WQS variance often evaluates a single parameter 

for a single permittee for a limited period of time. The level of effort a state or authorized tribe needs to 

devote to a WQS variance will in large part be determined by the complexity of the water quality 

problem the state or authorized tribe seeks to address.

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B. The Provision Allowing a Water Quality Standards Variance for Restoration 

Activities Should be Moved to Section 131.10(k) 

Commenters said that EPA should move the provision allowing a WQS variance for restoration activities 

to section 131.10(k). EPA disagrees with this comment. Section 131.14(b)(2)(i)(2) provides for a WQS 

variance to undertake actions necessary to facilitate lake, wetland, or stream restoration through dam 

removal or other significant reconfiguration activities that preclude attainment of the designated use 

and criterion while the actions are being implemented. EPA intends for this provision to be time-limited.

Section 131.10(k) pertains to designated uses that are not time-limited. Furthermore, the commenters 

do not explain the purpose of such a revision.

C. The Rule Should Include Additional Factors That Can Be Used to Justify a 

Water Quality Standards Variance

Commenters said that EPA should expand the availability of WQS variances. For example, commenters 

said EPA should add an additional factor that would justify a WQS variance for a natural disaster that 

causes significant damage to a water body or climate conditions that cause the impairment of a water 

body for a period of several years. EPA considered expanding the list of factors justifying a WQS variance 

(beyond the addition of the factor related to restoration activities) but concluded that the current list 

was as comprehensive as necessary as it stands. For example, section 131.10(g) already includes factors 

that satisfy circumstances related to natural conditions or low flows, and the factor at section

131.10(g)(3) generally addresses human-caused conditions that cannot be remedied. Under appropriate 

circumstances and with proper demonstration, these factors could address the examples suggested by 

the commenters.

Commenters said the requirements for a WQS variance “would preclude the availability of a variance 

while the state agency develops site-specific criteria.” EPA disagrees with these commenters. The final 

rule does not preclude a state or authorized tribe from utilizing a WQS variance when the state or 

authorized tribe is studying or developing site-specific criteria provided the WQS variance is consistent 

with the requirements at section 131.14.

Commenters said of the new restoration factor proposed at section 131.14(b)(2)(ii), “Actions necessary 

to facilitate restoration through dam removal or other significant wetland or stream reconfiguration 

activities...,” should include water conservation activities. Commenters also said that EPA should revise 

the rule to allow a WQS variance “for any activity whose primary purpose is restoration of a waterbody.” 

EPA agrees that the proposed new restoration factor should be expanded and did so in the final rule but 

only to include the word “lakes” such that section 131.14(b)(2)(i)(A)(2) now reads: “Actions necessary to 

facilitate lake, wetland, or stream restoration through dam removal or other significant reconfiguration 

activities...” However, EPA does not agree that specifically including water conservation activities is 

necessary because the current factors address that concern. Commenters also do not adequately 

explain why the existing factors in section 131.10(g) are inadequate. For example, commenters said: 

“water conservation activities also will necessitate a time-limited lowering of water quality and the 

language of this provision should be redrafted to encompass this circumstance as well. For example, 

many California cities have been observing an increase in pollutant concentrations entering wastewater 

treatment plants as flow is reduced (due in part to water conservation activities) but mass remains the 

same.” A state or authorized tribe may justify a WQS variance under such circumstances on the basis of 

section 131.10(g)(5), “Physical conditions related to the natural features of the water body, such as the 

lack of a proper substrate, cover, flow, depth, pools, riffles, and the like, unrelated to water quality, 

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preclude attainment of aquatic life protection uses,” or section 131.10(g)(6), “Controls more stringent 

than those required by sections 301(b) and 306 of the Act would result in substantial and widespread 

economic and social impact.” 

Some commenters said the rule is generally too strict and that “Other factors that would warrant a 

variance should be included, such as technical feasibility, competing stakeholder variances, and other 

watershed activities.” In the past, states and authorized tribes have justified a WQS variance due to

“technical feasibility” issues by citing section 131.10(g)(6), “Controls more stringent than those required 

by sections 301(b) and 306 of the Act would result in substantial and widespread economic and social 

impact.” In those circumstances, the state demonstrated that the only way to meet strict permit limits is 

to implement expensive pollutant controls such as reverse osmosis and that such controls result in 

substantial and widespread economic and social impact. Without further description from commenters 

of what “competing stakeholder variances” means, it is difficult to envision the specific scenario 

contemplated. However, as a general matter, if there is competition for use of the resource, the state or 

authorized tribe could use the list of factors in place for the final rule to effectively guide the 

determination of attainability. Commenters suggesting the rule should include factors to allow WQS 

variances for “other watershed activities” do not describe the watershed activities to include, but EPA 

cannot think of limiting watershed activities that would not be covered by the factors in place for the 

final rule. 

Commenters said the rule should provide for a WQS variance for “other water quality improvement 

efforts that do not entail physical modification of a water (e.g., addressing a seep from historic mining 

activities).” EPA disagrees with these commenters. Such a scenario appears to already be covered under 

section 131.10(g)(3), “Human caused conditions or sources of pollution prevent the attainment of the 

use and cannot be remedied or would cause more environmental damage to correct than to leave in 

place.” 

D. The Rule Should Specify the Procedures and Level of Effort Needed to 

Utilize Water Quality Standards Variances

Commenters said: “specific procedures, effort, and time [should] be indicated for achieving variances.” 

The CWA provides state and authorized tribes with primary responsibility for administering their WQS 

program and assigns EPA with oversight responsibility. Most states and authorized tribes individually 

tailor their WQS procedures and processes to suit their own administrative structure. EPA cannot 

speculate on the procedures and level of effort any one state or authorized tribe will require to adopt 

and submit a WQS variance. The preamble to the final rule provides some guidance on general issues in 

response to public comments to the proposed rule. EPA encourages states and authorized tribes to work 

with their EPA regional office, stakeholders, and public to establish an administrative process to utilize 

WQS variances effectively and efficiently. The economic analysis (EA) to the final rule also provides 

national average estimates of the level of effort and cost associated with several of the requirements in 

the final rule related to WQS variances.

E. The Rule Should Remove Some of the Factors That Can Be Used to Justify a 

Water Quality Standards Variance

Commenters said that several of the factors listed in section 131.10(g) are not relevant to WQS 

variances and thus should be removed. EPA disagrees with these commenters. Although states and 

authorized tribes may justify the majority of future WQS variances using a subset of the six factors listed 

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in section 131.10(g), EPA cannot speculate on all the possible circumstances where a state or authorized 

tribe may appropriately utilize a WQS variance. The commenters do not explain, and EPA does not see 

the purpose of, removing any of the factors listed in section 131.10(g).

F. EPA Should Not Require Use of 1995 Economic Guidance to Justify a Water 

Quality Standards Variance

Commenters said EPA should not require states and authorized tribes to use its March 1995 Interim 

Economic Guidance for Water Quality Standards as a basis for determining whether an individual WQS 

variance has widespread “social and economic impact.” EPA does not require use of this guidance to 

meet the regulatory requirements. States and authorized tribes may use alternative approaches, subject 

to EPA review based on the regulatory requirements themselves. EPA’s Interim Economic Guidance for 

Water Quality Standards Workbook was developed to help consider economics at various points in the 

process of setting or revising WQS. The usefulness this guidance document is beyond the scope of this 

final rule.

G. Strike out Regulatory Text

Commenter suggested striking out section 131.14(b)(2) that limits the requirement to justify a WQS 

variance based on the factors in 131.10(g) to variances for 101(a)(2) uses. Specifically, the commenter 

suggested the following revisions to the regulatory text: “(2) The State must submit a demonstration 

justifying the need for a WQS variance [begin new text] by showing. [end new text] [begin strikeout] For 

a WQS variance to a use specified in section 101(a)(2) of the Act or a sub-category of such a use, the 

State must submit a demonstration [end strikeout] that attaining the designated use and criterion is not 

feasible during the term of the WQS variance because: “ 

EPA carefully considered this comment and concluded it was reasonable and authorized by the CWA to 

distinguish between 101(a)(2) and non 101(a)(2) uses in establishing the requirements for a variance. As 

explained in the preamble to the final rule, the CWA distinguishes between these two broad categories 

of uses and EPA has implemented the CWA to distinguish between these two categories. Consistent 

with section 101(a)(2) of the Act, EPA concluded it was appropriate to limit the requirement for showing 

attainability to 101(a)(2) uses. See below for further discussion. See also response Essay 5.h for a 

discussion of EPA’s rationale for not requiring use of the 131.10(g) factors for use removal for non101(a)(2) uses.

H. Uses Not Specified in Section 101(a)(2) of the Clean Water Act

Commenters said that removing the requirement that states and authorized tribes justify a WQS 

variances to non 101(a)(2) uses such as drinking water and wild rice by demonstrating the use is not 

attainable due to at least one of the six factors specified in section 131.10(g) will weaken protections for 

those uses. The CWA makes a distinction between 101(a)(2) uses and non 101(a)(2) uses and ties 

“wherever attainable” to the former category and ties “consideration of the use and value” to both 

categories. Consistent with section 101(a)(2), EPA chose to limit to 101(a)(2) uses the requirement for 

demonstrating that attaining the designated use and criterion is not feasible because of one of the 

factors listed in section 131.10(g). As such, the final rule best reflects a reasonable implementation of 

the CWA. The final rule also clarifies that while states and authorized tribes are not required to 

demonstrate non-attainability based on one of the six factors in section 131.10(g) when adopting a WQS 

variance to a non 101(a)(2) use, the state or authorized tribe must meet the requirements in section

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131.10(a) to submit documentation justifying how they have considered the use and value of a water.

EPA determined that the “use and value demonstration” implemented the provision in section 

303(c)(2)(A) to take into consideration the use and value of waters for various uses when adopting WQS.

EPA concluded that the use and value demonstration will still provide adequate protections in 

evaluating whether to adopt a variance for a non 101(a)(2) use. While a “use and value demonstration” 

provides a level of discretion to states and authorized tribes in determining whether to adopt a variance 

for a non 101(a)(2) use, EPA believes that the nature and variety among the non 101(a)(2) uses justifies 

this flexibility for states and authorized tribes to describe the use and value of such uses, after a public 

process consistent with section 131.20(b), just as any new or revised WQS. See also response Essay 5.h 

for a discussion of EPA’s rationale for not requiring use of the 131.10(g) factors for use removal for non101(a)(2) uses. For additional discussion on what is required when removing or revising non 101(a)(2) 

uses (i.e., a “use and value demonstration”), see section II.B of the preamble to the final rule. 

Commenters also said: “This element of EPA’s proposal is a very significant weakening of CWA 

requirements that will have serious impacts on fish, aquatic plants and wildlife.” EPA disagrees with this 

comment. To the extent that criteria in place to protect a non 101(a)(2) use such as public water supply, 

agricultural, or industrial uses also provide protection for fish, aquatic plants, and wildlife, EPA would

expect the state or authorized tribe to adopt the WQS necessary to specifically protect those designated 

uses, and not inadvertently leave them unprotected by a removal of a non-101(a)(2) use. That is, a state 

or tribe should protect CWA 101(a)(2) uses through the adoption of such uses and criteria to protect 

such uses.

I. The Term “Feasible” Should Not Be in the Rule

Commenters said: “The term “feasible” should not be included in the Proposed Rule. Establishing a 

feasibility requirement is contrary to CWA Section 301(b)(1)(C), which requires that water quality 

standards be met without regard to cost or feasibility when applying water quality based effluent 

limitations (“WQBELs”). See, e.g., Upper Blackstone Water Pollution Abatement Dist. v. EPA, 690 F.3d 9, 

33 (1st Cir. 2012).” EPA disagrees with this comment. The term “feasible” is used in section 131.10(g).

The feasibility of meeting WQS as provided in section 131.10(g) have been in effect since 1983, and EPA 

sees no reason to deviate from these long established principles. While CWA 301(b)(1)(C) does not 

include a provision for including “feasible” in deriving water quality-based effluent limits (WQBELs) to 

meet the applicable WQS, such a consideration is appropriate in adopting the WQS.

J. Add Regulatory Text

Commenters suggest adding to the proposed section 131.14(b)(2) the regulatory text: “the State must 

meet the requirements of § 131.10(d) and (e), and must demonstrate that...”. EPA determined it is not 

necessary to add these provisions to section 131.14. The new rule does include requirements similar to 

the requirements related to technology-based requirements in section 131.10(d) at section 131.14(a)(4) 

and includes a requirement requiring identification and documentation of “cost-effective and 

reasonable BMPs for non-point sources” for WQS variances applicable to a water body or waterbody 

segment at section 131.14(b)(2)(iii). EPA provided it’s rationale in the preamble to the proposed rule for 

why the requirement in section 131.10(d) for use changes was not carried forward to WQS variances

verbatim. Specifically, the preamble states: “The EPA’s proposed requirement for waterbody variances 

differs from those applicable to designated uses because variances are time-limited and targeted serving 

as a tool to facilitate progress toward the designated use and criterion. It is unnecessary to require 

states and tribes to demonstrate that the designated use and criteria are unattainable even if cost 

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effective and reasonable best management practices (BMPs) were implemented, as is required when 

revising a designated use, because variances do not ‘‘permanently’’ downgrade the designated use but 

establish a regulatory mechanism by which feasible progress will be made during the term of the 

variance. Instead, a requirement to identify and document cost-effective and reasonable BMPs for other 

sources will assist states and tribes in identifying the actions they may need to implement to meet their 

interim requirements as well as to make feasible progress towards attaining the designated use and 

criterion.” (78 FR 54536, September 4, 2013). EPA still considers this to be a valid rationale. Additionally, 

EPA is deleting section 131.10(e) in the final rule in a conforming edit as it may appear to be in conflict 

with public participation requirements at section 131.20(b). See section II.G of the preamble to the final 

rule for EPA’s rationale for changes related to section 131.10(e). EPA requires WQS variances to be 

subject to the same public participation requirements as any other WQS per section 131.20(b).

Commenters said: “The EPA is proposing to add a new factor to address the situation when a timelimited exceedence of a criterion might be expected while efforts for dam removal or significant 

wetlands or stream reconfiguration/ restoration efforts are underway to facilitate restoration of the 

natural physical features of a waterbody. Where is this referenced in the updated rule? § 131.10(g) 

appears to still only contain six factors.” The factor is specified in section 131.14(b)(2)(I)(A)(2).

Commenters said: “Section F.2.b.ii. lists things to be considered when making a demonstration for 

“Human Caused Conditions...” under § 131.10(g)(3). WDNR would like to recommend putting those 

5 considerations in the rule itself rather than just in the pre-amble.” EPA does not consider that such 

additions are necessary or appropriate in the regulatory text. The discussion of these factors in the 

preamble sets for EPA’s position on these factors.

K. Support and Interpretation of the Proposed Rule

EPA notes that several commenters provided their support for the proposed rule in relation to the 

requirements for supporting documentation and others described their interpretation of the proposed 

rule.

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Essay 8.g.v – Variances Submission Requirements: Identification and 

Documentation of BMPs for NPS

A. Nonpoint Source Requirements Exceed EPA’s Authority

Some commenters stated that the U.S Environmental Protection Agency’ (EPA’s) requirement in the 

proposed rule at section 131.14(b)(3) requiring identification and documentation of best management 

practices (BMPs) for nonpoint source (NPS) controls as supporting documentation for a waterbody 

variance exceeded EPA’s Clean Water Act (CWA) authority and was inconsistent with Congressional 

intent. Commenters stated that the rule’s mandate to identify NPS controls that could be implemented 

is not authorized under CWA section 303(c). That EPA’s sole authority relating to identification of NPS 

controls is in CWA section 319. EPA does not agree with the commenters’ interpretation of the CWA.

Section 101(a)(7) of the Act provides that “... it is the national policy that programs for the control of 

nonpoint sources of pollution be developed and implemented in an expeditious manner so as to enable 

the goals of this Act to be met through the control of both point and nonpoint sources of pollution.” In 

1987 Congress added section 319 to the CWA to increase the focus on addressing NPS pollution in 

recognition of the significant impact that NPS have on the nation’s waters. However, section 319 is not 

the only program under the CWA that addresses NPS pollution. The section 303(d) total maximum daily 

load (TMDL) program is a clear example. CWA section 303(d) has been a part of the CWA since 1972. It 

requires that states identify waters not meeting water quality standards (WQS) and establish TMDLs for 

those waters whether the waters are impaired by point sources, NPS or a combination of both. TMDLs 

include load allocations for NPS (Title 40 of the Code of Federal Regulations (CFR) section 130.7). If 

wasteload allocations (WLA) for point sources are to be made less stringent based on assumed 

reductions by NPS, the states must provide reasonable assurance that the NPS reductions will occur.

EPA’s interpretation of section 303(d) to include consideration of NPS pollution has been upheld and 

EPA’s implementation of those provisions have been upheld judicially. Prosolino v. Nastri, 291 F.3d. 1123 

(9th Cir. 2002); see also American Farm Bureau Federation v. EPA, ___F.3d _ (3d.Cir. 2015). The 

requirements in the final rule regarding identification and documentation of NPS BMPs is consistent 

with Congressional intent and within EPA’s authority under the CWA.

Some comments asserted that EPA’s rule was an attempt to exert authority over NPS and compel 

implementation of NPS controls. Another commenter said that EPA’s rule would “federalize” NPS 

controls. EPA’s rule requires the identification and documentation of BMPs for NPS controls for WQS 

variances applicable to a water body or waterbody segment. EPA’s rule does not compel or require the 

implementation of such controls. But EPA’s rule reasonably does require the consideration of NPS 

contributions and cost-effective and reasonable BMPs to address those contributions in deciding 

whether a WQS variance is appropriate. Additionally, for a subsequent WQS variance applicable to a 

water body or waterbody segment, EPA’s final rule also reasonably requires the state or authorized tribe 

to “include documentation of whether and to what extent best management practices for nonpoint 

source controls were implemented to address the pollutant(s) or water quality parameter(s) subject to 

the WQS variance and the water quality progress achieved.” Again, this documentation is needed so 

that EPA and the public can understand what solutions to the water quality challenge that the state or 

authorized tribe has tried prior to a subsequent WQS variance. See also response Essay 8.i for discussion 

on “renewal” or “subsequent” WQS variances.

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Other commenters urged that EPA’s rule be limited to identifying and documenting only those BMPs 

that are required under state law. Commenters expressed concerns that EPA’s proposed rule could be 

“misinterpreted to improperly bootstrap a requirement for BMPs not otherwise required as a condition 

of the variance.” They recommended that section 131.14 (b)(3) refer to cost-effective and reasonable 

BMPs for NPS controls otherwise required by law. 

EPA recognizes that the CWA gives states and authorized tribes discretion on how to control pollution 

from NPS. Importantly, WQS established pursuant to CWA section 303 apply to the water bodies 

themselves, regardless of the source(s) of pollution/pollutants. WQS express the desired condition and 

level of protection for a water body. EPA determined that in the context of developing appropriate 

regulations for adoption of WQS variances applicable to a water body or waterbody segment as new or 

revised WQS, it was both important and necessary to take NPS into account. EPA further determined 

that it was important to include in the requirement to identify and document BMPs for NPS controls all 

cost-effective and reasonable BMPs, not just those currently required by state or tribal law. To restrict 

the BMPs in such a way would remove, even from consideration, BMPs that may be the most costeffective and appropriate BMPs. Consistent with the objectives of WQS variances, to improve water 

quality moving toward ultimate attainment of the underlying WQS, it was reasonable to include the 

broader requirement in the final rule. 

Some commenters expressed concern that the rule implies that point source permittees would be 

required to implement NPS controls as a part of their permit conditions if the discharge is to a 

waterbody that has an approved WQS variance. The final rule includes no implications regarding what 

sources will be required to implement BMPs for NPS controls. EPA expects that a state or authorized 

tribe will decide which entities with control over NPS may be asked to take actions and what those 

actions might be depending on the facts of the specific WQS waterbody variance. Other commenters 

suggested that EPA revise the rule to replace the requirement regarding identification and 

documentation of BMPs with a requirement that states and authorized tribes identify an adaptive 

management framework that could be implemented to make progress towards attaining the designated 

use and criterion and for renewal that the rule provide that the state submit documentation that 

reasonable progress is being made to address the pollutant(s) subject to the WQS variance during the 

WQS variance period. Adaptive management is an important feature of WQS variances. The time 

provided by WQS variances allows for adaptive management efforts to be implemented. That said, EPA 

did not agree with the commenters’ suggestion to remove references in the rule to NPS BMPs and only 

include a general reference to adaptive management. EPA concluded it was important to specifically 

focus on NPS in the context of WQS variances applicable to a water body or waterbody segment in order 

to ensure that states and authorized tribes will bring consideration of BMPs for NPS to the forefront of 

their decision-making and development of any such WQS variance. This is the case in both the initial 

adoption of the WQS variance and any consideration on whether to adopt a subsequent the WQS 

variance. The requirement will also ensure that the public is provided the opportunity to evaluate and 

comment on how a state or authorized tribe are taking such considerations into account.

Commenters also said: “EPA cannot base variances for point source dischargers on conditions 

concerning the implementation of nonpoint source controls.” The final rule does not base WQS 

variances for point source dischargers on implementation of NPS controls. That said, the rule does 

include information regarding NPS and the implementation of controls for such sources as one piece of 

information that is relevant to evaluating the appropriateness of those WQS variances applicable to a 

water body or waterbody segment.

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B. “No Control” over Nonpoint Source Controls

Commenters expressed concern that states and authorized tribes would be required to list BMPs for 

sources over which they have no regulatory authority. Similarly some commenters said that because a 

state or authorized tribe does not regulate NPS of pollution, identification and documentation of any 

cost-effective and reasonable BMPs for NPS controls cannot occur. EPA considered these comments 

carefully but concluded that, for WQS variances applicable to a water body or waterbody segment, it is a 

reasonable requirement that states and authorized tribes identify and document BMPs for NPS even if 

the state or tribe does not regulate those sources. The state and tribal water quality agencies are 

responsible for understanding and evaluating the waters within their jurisdictions. Under CWA section 

303(d) states and authorized tribes must assess and identify waters not meeting WQS and develop 

TMDLs for those waters even if the waters are impaired solely by NPS. EPA acknowledges that some 

states and authorized tribes may not regulate NPS of pollutants. However, the final rule does not 

compel states and authorized tribes to implement NPS controls or otherwise regulate NPS of pollutants.

Another commenter suggested revisions to the regulatory text specifying that, for a waterbody variance, 

the state must identify and document any cost-effective and reasonable BMPs for NPS controls under 

the control of the discharger that could be implemented to make progress towards attaining the 

designated use and criterion. One commenter expressed concerns that failure of a state agency to 

address the NPS requirements could penalize point sources by delaying issuance of variances. For the 

reasons discussed above, EPA concluded against including language in the final rule limiting the scope of 

BMPs that states and authorized tribes would need to identify and document. For WQS variances 

applicable to a water body or waterbody segment, often NPS will not be under the control of a 

discharger subject to a National Pollutant Discharge Elimination System (NPDES) permit. For discharger 

specific variances, any consideration of BMPs would be expected to be those under the control of the 

discharger. Regarding the final comment raising concern in delay of issuance of a variance, while the 

requirement to identify and document BMPs will add some time, EPA believes it is warranted by the 

benefits of having and considering that important information in the development of the WQS variance.

C. Identification and Documentation of Nonpoint Source Best Management 

Practices Should Be the Responsibility of Government Entities, Not Permittees

A commenter (a municipal discharger) expressed support for the requirement to identify and document 

BMPs for NPS but also expressed concern the state may might require dischargers to develop (or pay to 

develop) the information. The commenter requested that the final rule specifically indicate it is the 

responsibility of the state governments to develop this information and not third parties that are not 

NPS dischargers. EPA decided it was not necessary or appropriate to include such a restriction in the 

final rule. The state or authorized tribe is in the best position to decide how to develop the necessary 

information. This is no different from the discretion that is left to the states and authorized tribes in 

adopting other WQS. 

D. Commenter Provides Interpretation of the Proposed Rule

EPA thanks the commenters for describing their interpretation of the proposed rule. Public descriptions, 

interpretations, and perceptions of the proposed rule help EPA improve clarity and ensure the final rule 

accomplishes EPA’s goals and objectives.

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E. Strike out Regulatory Text

A commenter suggested striking proposed section 131.14(b)(3) [the provision requiring identification 

and documentation of cost-effective and reasonable BMPs for NPS]. The commenter stated that the 

CWA does not include any provision “to require or enforce best management practices for nonpoint 

source controls.” The commenter further stated that “EPA’s proposal could be misinterpreted to impose 

such a requirement.” 

EPA carefully considered this comment. EPA’s proposed (and final) rule neither require nor enforce 

BMPs for NPS controls. EPA’s final rule does require that in evaluating whether to adopt a WQS variance 

applicable to a water body or waterbody segment, the state or authorized tribe, and the public, consider 

pollutant contributions from NPS and to identify and document cost-effective and reasonable BMPs that 

could be used to control those NPS. Those are relevant considerations in determining the highest 

attainable condition (HAC) and the appropriate term for any such WQS variance and ultimately whether 

to adopt such a WQS variance.

Other commenters suggested the following revisions to the proposed rule section on renewals to 

eliminate the requirement regarding BMPs for NPS: “(d) WQS variance renewals: EPA may approve a 

WQS variance renewal if the State meets the requirements of this section and provides documentation 

of the actions taken to meet the requirements of the previous WQS variance. [begin strikeout] For a 

waterbody WQS variance renewal, the state must also provide documentation of whether and to what 

extent BMPs have been implemented to address the pollutant(s) subject to the WQS variance and the 

water quality progress achieved during the WQS variance period. [end strikeout] Renewal of a WQS 

variance may be disapproved if the applicant did not comply with the conditions of the original WQS 

variance, or otherwise does not meet the requirements of this section.” 

EPA also rejected this proposed revision because, as discussed above, EPA concluded that it is important 

to consider the contributions from NPS and what cost-effective and reasonable BMPs exist is deciding 

whether to adopt a WQS variance applicable to a water body or waterbody segment and what solutions 

to the water quality challenge have been tried (including those related to NPS BMPs) prior to adoption 

and approval of a subsequent WQS variance.

Comments further suggested that: “EPA should remove any procedural or substantive requirements 

relating to nonpoint sources or state and tribal purview over those sources from the Proposed Rule, and 

clarify (as it has in the past) that intervening in state and tribal decisions regarding nonpoint sources 

would go beyond EPA’s authority under the CWA.” 

As discussed in other sections of this comment response essay, EPA is not acting beyond its authority 

under the CWA in adopting the provisions in the final rule regarding identification and documentation of 

BMPs for NPS control.

F. Include a Requirement That States Evaluate the Effectiveness of Best 

Management Practices Implemented

Commenters said that EPA should “include a requirement that states evaluate the effectiveness of any 

BMPs that were implemented during the previous variance period and make recommendations for 

improvements to the BMP program that are appropriate, if any.” EPA disagrees with these commenters. 

Although EPA acknowledges that evaluating the effectiveness of BMPs and improving state or tribal NPS

control programs is good practice, requiring such an evaluation is beyond the scope of this final rule.

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G. For Variance Renewals, the Level of Proof Required to Document Whether 

and to What Extent Best Management Practices for Nonpoint Source Controls 

Were Implemented Is Not Adequately Defined or Explained

Commenters said: “EPA should eliminate its proposed requirement that States must submit adequate 

proof regarding use of best management practices for nonpoint source controls to address pollutants 

subject to the variance, as well as the water quality progress achieved during the variance period. The 

level of proof required is not adequately defined or explained and will likely be interpreted 

inconsistently among EPA’s regions. Moreover, such a burden will undoubtedly force States to dedicate 

significant resources to conduct engineering and scientific studies, as well as regulatory negotiation and 

even litigation, all to justify the continuance of a variance the State-the entity Congress tabbed as the 

one with primary responsibility for establishing and implementing WQS-deems necessary.” Other 

commenters said: “the provision again will invite wasteful and time consuming litigation in connection 

with any variance request or approval because what constitutes a “reasonable” method to address nonpoint sources is a highly subjective policy matter.” 

The final rule at section 131.14(b)(2)(iii)(B) specifies that any subsequent WQS variance applicable to a 

water body or waterbody segment must include documentation of whether and to what extent BMPs 

for NPS controls were implemented to address the pollutant(s) or water quality parameter(s) subject to 

the WQS variance and the water quality progress achieved. EPA believes that such information is 

important for the states and authorized tribes as well as all the interested stakeholders to have in 

evaluating whether it is appropriate to adopt a subsequent WQS variance and what the conditions of 

any such WQS variance should be. EPA determined that it was best to leave to the states, tribes and 

public in the first instance to determine how best to document this information. It will be a case-by-case 

determination. While there may be issues, and possibly even disputes, over what documentation will be 

provided and what decisions to make from that information that is not a justification for eliminating the 

requirement to develop and consider this important information in deciding whether to adopt a 

subsequent WQS variance applicable to a water body or waterbody segment. 

H. Add Regulatory Text

Commenters said: “The preamble makes clear that it is not necessary to implement these [BMP] 

measures, but merely to identify them and inform the public of them. See 78 Fed. Reg. at 54535-56. The 

AMA supports this limited use of any such information, but believes it should be stated more clearly in 

the rule text (e.g., by adding “for information purposes only” after “identify and document” in the first 

paragraph of proposed 40 C.F.R. § 131.14(b)(3)).” EPA does not agree that such a revision to the rule is 

final necessary or should be made. EPA acknowledges that the CWA does not establish a regulatory 

program for NPS. And the final rule does not require states or authorized tribes to regulate NPS. 

However, as discussed in the preamble section cited by the commenter, EPA emphasized that it was 

“essential for states and authorized tribes to consider and provide information to the public regarding 

the impact that controlling other sources application of cost-effective and reasonable BMPs could have 

on water quality before granting a waterbody variance” (78 FR 54535). EPA considers the words 

“identification and documentation” to be clear and do not imply any requirement to regulate NPS. At 

the same time, the commenter’s suggested revision could add confusion by implying that there is no 

expectation that actions will be taken based on the identification and documentation of BMPs for NPS 

control.

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I. Add an Additional Public Process

Commenters said: “the proposal further requires that the state must provide public notice and 

comment for this documentation. Given that the variance itself is subject to public participation 

requirements (as specified in the first sentence of 40 C.F.R. § 131.14), and that the BMPs are being 

identified for information purposes only, it is not clear why a separate public process is required. The 

AMA questions the need for this additional process.” EPA does not intend that that a separate public 

process must be provided for the public to review of documentation on BMPs for NPS control. The 

intent of including the provision that “A State must provide public notice and comment on any such 

documentation” was to make clear that this documentation would be part of any record for a WQS 

variance applicable to a water body or waterbody segment made available to the public for review and 

comment. The final rule does not require an additional public process from the process the state or 

authorized tribe uses to adopt the WQS variance. States and authorized tribes can choose to satisfy the

public process specified in (b)(2)(iii)(A) during the same public process that satisfies the public 

participation requirements at section 131.20(b). 

J. What Happens If Best Management Practices Are Not Implemented?

Commenters requested EPA explain what happens in the event that BMPs are not implemented. The 

purpose of any WQS variance is to make progress toward meeting the underlying WQS. It is EPA’s 

current position that when deciding to adopt a WQS variance (including a subsequent WQS variance) 

applicable to a water body or waterbody segment, it is important for states and authorized tribes to 

consider all pollutant sources, and to ensure that the public fully understands the reasons why a WQS 

variance is necessary and for how long. EPA expects that in most cases, states and authorized tribes will 

adopt a WQS variance applicable to a water body or waterbody segment when pollutant sources 

originate from both point and NPS, and all stakeholders are working together reduce pollutant loads and 

restore the water body. The issue of what happens if BMPs are not implemented could arise in the 

context of a state or authorized tribe justifying the term of such WQS variance applicable to a water 

body or waterbody segment or during the re-evaluation of the HAC for such a WQS variance with a 

duration greater than five years or when deciding whether to adopt a subsequent WQS variance. The 

final rule’s requirement to identify and document BMPs for NPS and to document to what extent BMPs 

were implemented and the water quality progress achieved is to ensure that this important information 

be a consideration in making the decision about the duration of the WQS variance, the HAC, and

whether to adopt a subsequent WQS variance and the term and conditions for any such WQS variance. 

How that information will be considered will be a case-by-case decision. EPA concluded it was not 

necessary or appropriate to address that issue in the final rule’s regulatory text. 

K. The Requirements for a Waterbody Variance Are Overly Burdensome and 

Provide a Disincentive to Its Use

The commenter stated they did not disagree that all sources of a pollutant should be evaluated to 

address relevant reductions, but thought the requirements in the rule related to BMPs for NPS control 

are overly burdensome and a disincentive to its use. The commenter said that the information required 

by the rule are better suited for the TMDL process.

EPA’s position is that the requirements in the final rule related to WQS variances applicable to a water 

body or waterbody segment and BMPs for NPS controls carefully balance the flexibility states and 

authorized tribes need to effectively utilize these WQS variances, with the accountability and 

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transparency the public needs to be assured that WQS variances are used appropriately. EPA 

acknowledges that developing and implementing this type of WQS variance can involve considering 

information similar to that considered in developing a TMDL in some situations. Nevertheless, EPA has 

concluded that the information regarding the identification and documentation of BMPs for NPS 

controls is necessary and important to meaningfully consider whether a WQS variance applicable to a 

water body or waterbody segment is appropriate and the term and conditions for such a variance. EPA is 

committed to working with states and authorized tribes to make this provision work efficiently and 

effectively. See EPA’s Economic Analysis for the final rule for more information on EPA’s burden 

estimates.

L. The Best Management Practices for Nonpoint Source Controls Provision 

Should Apply to All Variances

Commenters said: “We support EPA’s proposed rule that would require states to identify and document 

any cost effective and reasonable best management practices (BMP) for nonpoint sources related to the 

pollutant(s) and location(s) specified in a variance. It is unclear why EPA restricts this requirement to 

waterbody variances and we strongly urge that any such provisions apply to all variances. The same 

need as EPA establishes in the preamble for waterbody variances is needed for variances issued to 

individual dischargers in any situation where nonpoint sources are a primary or even major contributor 

to impairment.” 

EPA does not agree that the NPS related provision should apply to all WQS variances. Individual 

dischargers qualified to receive a WQS variance are usually addressing facility-specific water quality 

challenges that prevent them from meeting the water quality-based effluent limit (WQBEL) in their 

NPDES permit. EPA believes that requiring states and authorized tribes to identify and document costeffective and reasonable BMPs for NPS controls for every discharger-specific WQS variance would be a 

disincentive to utilizing WQS variances to make water quality progress, and instead result in states and 

authorized tribes permanently removing designated uses. On the other hand, situations where a WQS 

variance applicable to a water body or waterbody segment is appropriate will likely involve multiple 

sources of pollutants. In such cases, understanding all the sources of pollutants (both point and 

nonpoint) ensures the public understands the role NPS play in the water body or waterbody segment 

that will receive the WQS variance, is an important first step to determining the actions necessary to 

make progress toward attaining the underlying WQS. 

M. The Rule Does Not Adequately Require Controls for Nonpoint Sources of 

Pollutants

Commenters urged that the final rule require that BMPs for NPS controls be implemented. One 

commenter said: “EPA completely skirts the question of how this information it proposes be derived on 

BMPs will be used. Despite EPA’s repeated suggestions that variances will be used to move waters 

towards full attainment, EPA does not require that these identified BMPs be used as part of the variance 

nor that failure to use them over the course of the variance can and will be considered in whether the 

variance will be reissued. Instead, the proposed rule merely states that a state ‘must also provide 

documentation of whether and to what extent BMPs have been implemented.’ Proposed 40 C.F.R. 

§ 131.14(d). This relegates the BMPs to a status of being interesting but unhelpful in improving water 

quality.” 

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A commenter also said: “if EPA keeps the waterbody variances it must make implementation of 

nonpoint source controls mandatory. Otherwise, point sources will continue to demand and receive 

variances in large part because nonpoint sources are not doing their share of pollution controls, an 

endless cycle never to be broken.” 

Finally, a commenters suggested that proposed section 131.14(b)(3) be amended to read as follows: 

“[begin strikeout] For a waterbody variance,[end strikeout] The state must identify and document [begin 

strikeout] any [end strikeout] [begin new text] all [end new text] cost-effective and reasonable best 

management practices for nonpoint source controls related to the pollutant(s) and location(s) specified 

in the WQS variance that could be implemented to make progress towards attaining the designated use 

and criterion. [begin strikeout] A State must provide public notice and comment for any such 

documentation. [end strikeout] [begin new text] The BMPs identified must be readily measurable. The 

state must provide a plan for achieving implementation of the identified BMPs including timeframes for 

their achievement, methods of assuring their implementation, and a monitoring plan to evaluate 

implementation. This plan will constitute conditions of the variance that apply to the state. [end new 

text]” 

EPA carefully considered all of these comments, but concluded that the final rule should not require 

implementation of BMPs for NPS controls. EPA believes that the final rule strikes the right balance 

between ensuring the appropriate information and data on BMPs for NPS controls are considered while 

also recognizing that states and authorized tribes have discretion in deciding how best to work with 

stakeholders to address NPS pollution. EPA believes that identification and documentation of any costeffective and reasonable BMPs for NPS controls will help ensure the public understands the role NPS

play in the waterbody or water body segment that is being considered for such a WQS variance. This is a 

critical first step toward addressing widespread water quality challenges. EPA intends for states and 

authorized tribes to utilize a WQS variance to a water body or waterbody segment in situations where 

both point sources and NPS work together toward the common goal of attaining the underlying WQS, 

which may include implementation of NPS controls. In addition, the requirement to identify and 

document cost-effective and reasonable BMPs for NPS controls increases public transparency by 

ensuring access to information about the potential need to control NPS of pollutants to attain the 

underlying WQS. Because of the collaboration needed to for a WQS variance applicable to a water body 

or waterbody segment, it is likely that the information regarding BMPs for NPS will be used to help 

justify the need for the WQS variance, justify the term of the WQS variance, or prove to be useful in 

future reevaluations (required for WQS variances with durations greater than five years).

In addition, contrary to commenters assertion that states and authorized tribes only consider BMPs 

“that are already required by law” the final rule specifies that states and authorized tribes consider any

[emphasis added] cost-effective and reasonable best management practices for nonpoint source 

controls. In this context, the EPA intends for the word “any” to mean not just those BMPs that may 

already be required by state regulations. The EPA notes that its interpretation of “any” in the final rule is 

distinct from the interpretation provided in the EPA’s 1994 Tudor Davies memorandum (“Interpretation 

of Federal Antidegradation Regulatory Requirement”) related to the antidegradation requirements. 

Section 131.12(a)(2) states that in allowing degradation of high quality water, “the State shall assure 

that there shall be achieved the highest statutory and regulatory requirements for all new and existing 

point sources and all cost-effective and reasonable best management practices for nonpoint source 

control.” The Tudor Davies memorandum clarifies that section 131.12(a)(2) does not require a state or 

authorized tribe to establish BMPs for NPS where such BMP requirements do not exist. Instead, the EPA 

interprets section 131.12 (a)(2) as requiring states and authorized tribes to adopt an antidegradation 

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policy that includes a provision that will assure that all cost-effective and reasonable BMPs established 

under state or tribal authority are implemented for NPS before that state or tribe authorizes 

degradation of high quality waters by point sources. That is, if the state or authorized tribe does not 

require NPS controls, then EPA cannot require the state or authorized tribe to establish BMPs for the 

NPS prior to allowing a lowering of high quality water. However, if the state or authorized tribe requires 

NPS controls, it needs to ensure those required controls are being implemented prior to allowing a 

lowering of water quality.

A commenter stated that: “In addition, to the extent that EPA believes that the mere identification of 

BMPs will assist in their being implemented, a position that we support as a first but inadequate step, it 

does that goal a disservice by not specifying what EPA will accept as BMPs that are ‘cost-effective and 

reasonable.’ EPA’s proposed rule language undermines this effort. In addition, EPA must ensure that the 

BMPs are clear, numeric, easy to determine if they are in effect or not, sufficient in number (i.e., more 

than one BMP may be required in tandem), and not, as footnote 29 mentions, just the BMPs that are 

already required by law.” Commenters also said: “There is every reason to expect states to simply refer 

to existing BMPs and perhaps not even explicitly but just by sister state agency. There is every reason to 

expect states to point to NRCS Field Office Technical Guides (“FOTG”) as what is “cost-effective and 

reasonable” even though the FOTGs are not clear and measurable and they were not developed to 

protect water quality. Also likely are references to various plans, none of which contain measurable 

BMPs. Without more detail in what EPA expects to see spelled out in the rule, EPA should expect the 

most vague, least protective, and least readily measured BMPs to be ‘identified and documented’ by the 

states.” 

EPA considered these comments and determined it was most appropriate to leave to the states and 

authorize tribes and their public processes how to define what BMPs will be considered cost-effective 

and reasonable. Those decisions will best be made on a case-by-case basis.

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Essay 8.g.vi – Variances Submission Requirements: Other Suggested 

Submission Requirements

A. Data Sufficiency for Demonstration of Unattainability 

Commenters said: “In regard to a Use Attainability Analysis (UAA), it is not clear what a “structured 

scientific assessment” requires, e.g., discharge monthly report (DMR) data or official scientific study by 

outside agencies. It is also not clear what objective quality evidence (OQE) is required to claim that the 

‘designated use and criterion are unattainable.’” and “does the intermittent monthly DMR data that 

shows exceedances suffice as QOE? Or will an official study be required?” and “EPA should allow the use 

of NPDES Permit DMR data as evidence to support a claim that a criterion is “unattainable” and thus 

request a WQS variance.” 

Commenters also said: “With regard to the documentation required from states for a variance, the 

proposal is excessive and looks very close to what would otherwise be required for a use attainability 

analysis (UAA). As EPA itself notes throughout the proposal, a variance is time-limited and “lies on top 

of” the otherwise applicable water quality standard for the water body in question. A variance is not a 

petition to change the designated use of a water body; therefore, the EPA should re-examine the criteria 

for a state to grant a variance, and refine the scope of documentation needed to reflect a variance’s true 

purpose.” 

Although there may be similarities between the analyses needed to justify removal of a designated use 

and the analyses needed to justify a water quality standards (WQS) variance, a WQS variance is likely to 

be significantly simpler and therefore less burdensome because the analysis is over a limited time 

period. The circumstances where a WQS variance may be justified are highly variable. The U.S. 

Environmental Protection Agency’s (EPA’s) position is that the final rule strikes the appropriate balance 

between requiring adequate information in the state/tribal submission to allow meaningful public 

participation and EPA review and to meet the intended objectives of WQS variances with providing 

sufficient flexibility for states and authorized tribes in their decision making and development of 

supporting documentation. EPA believes that states and authorized tribes need the flexibility to justify a 

WQS variance on a case-by-case basis, and prescribing precise data and analytical requirements in a 

federal rule would impede the utilization of WQS variances to make water quality progress.

The commenter should refer to EPA guidance on use attainability analyses or contact their regional 

office for more information about how to evaluate attainability in their particular circumstances. EPA 

directs the commenter to EPA’s previous guidance in the “Water Quality Standards Handbook” 

(http://water.epa.gov/scitech/swguidance/standards/handbook/index.cfm) as well as UAA case studies 

on EPA website at http://water.epa.gov/scitech/swguidance/standards/uses/uaa/. EPA notes that, as 

described by the commenter, National Pollutant Discharge Elimination System (NPDES) Permit DMR can 

be useful in informing a UAA; however, mere documentation of non-compliance with a water qualitybased effluent limit (WQBEL) from DMR alone will not be sufficient to support a demonstration based 

on one of the six factors in section 131.10(g) or the new restoration factor in section 131.14.

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Essay 8.h – Variances: Implementation

A. Revise Section 131.14(c) by Adding the Word “Effluent” before Limitations

One commenter suggested that the sentence in section 131.14(c) be revised to add the word “effluent” 

as follows: “Any effluent limitations required to implement the WQS variance shall be included in the 

NPDES permit for the permittee(s) subject to the WQS variance.” The U.S. Environmental Protection 

Agency (EPA) does not agree with the commenter’s suggested revision. The National Pollutant Discharge 

Elimination System (NPDES) permitting regulations provide that, in addition to effluent limitations, 

NPDES permits may contain special conditions to address unique situations. These special conditions 

include, but are not limited to, special studies, preventative requirements, best management practices

(BMPs), treatment practices, monitoring, reporting, and compliance requirements, and compliance 

schedules (CS). Circumstances where water quality standards (WQS) variances are utilized are by all 

intents and purposes unique situations. Adding the word “effluent” could inappropriately restrict the 

permitting authority’s discretion to include special conditions in the NPDES permit. Furthermore, the 

final rule provides an option to specify the highest attainable condition (HAC) as the greatest pollutant 

reduction achievable with the pollutant control technologies installed at the time the State adopts the 

WQS variance and the adoption and implementation of a pollutant minimization program (PMP). This 

option requires states and authorized tribes to adopt the PMP along with other elements that comprise 

the HAC. As part of the applicable WQS, the permitting authority would need to use the PMP (along with 

the quantifiable expression of the “greatest pollutant reduction achievable”) to derive NPDES permit 

limits and requirements. Requiring a PMP in circumstances where a discharger is already attaining the 

greatest pollutant reduction achievable helps ensure WQS variances are utilized to make progress 

toward the underlying designated use and not to simply maintain the status quo. EPA notes that some 

commenters stated support for the proposed requirement at section 131.14(c) and effective 

implementation of all variances or reiterated the regulatory text to show that they did not suggest 

changes to 131.14(c). See the final rule text at section 131.14(c) and subsection C of this essay for a 

discussion on how EPA revised section 131.14(c) based on comments.

B. Discussion of National Pollutant Discharge Elimination System Permits 

Leaves More Questions than Answers, Guidance Would Be Helpful

Commenters expressed confusion about how WQS variances relate to NPDES permitting. EPA revised 

the preamble to the final rule to better explain the relationship between WQS variances and NPDES 

permits. For a more detailed discussion, see response Essay 8.g.iii.

Commenters said guidance on how to include WQS variance conditions in NPDES permits would be 

helpful. A variety of guidance documents for NPDES permitting are available on EPA’s website. EPA can

also develop additional guidance as the need arises. 

C. Permit Conditions Must Be Enforceable

A commenter said: “The problem is that EPA has not established that variances must include any actions or 

conditions. Without a requirement for there to be conditions, yet other requirements that conditions be 

enforceable, and a requirement that conditions have been met in order to merit a renewal of a variance, 

EPA’s assurances of water quality improvements ring hollow.” Based on this and other comments, EPA 

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revised the section 131.14 regulations to ensure the final rule reinforces the requirements at 

section 122.44(d)(1)(vii)(A) by specifying that any limitations and requirements necessary to implement 

the WQS variance must be included as enforceable conditions of the implementing NPDES permit.

Furthermore, the preamble of the final rule explains that states and authorized tribes must justify the term 

of any WQS variance on the basis of the information and factors evaluated to justify the need for the WQS 

variance. States and authorized tribes must also describe the pollutant control activities, including those 

identified through a PMP, that the state or authorized tribe anticipates implementing throughout the WQS 

variance term to achieve the HAC. During its review of the WQS variance, EPA will evaluate this description 

of activities which must reflect only the time needed to plan activities, implement activities, or evaluate 

the outcome of activities. Explicitly requiring the state or authorized tribe to document the relationship 

between the pollutant control activities and the WQS variance term ensures that the term is only as long 

as necessary to achieve the HAC and that water quality progress is achieved throughout the entire WQS 

variance term. The pollutant control activities specified in the supporting documentation serve as

milestones for the WQS variance and inform the permitting authority when developing the enforceable 

terms and conditions of the NPDES permit necessary to implement the variance, as required at Title 40 of 

the Code of Federal Regulations (CFR) section 122.44(d)(1).

EPA agrees with commenters who suggested strengthening the regulatory language that requires 

implementation of the WQS variances in NPDES permits. One commenter suggested that EPA add

language to section 131.14(c) that would require: “Any BMPs identified in paragraph (b)(3) of this 

section that are within the scope of the permittee’s authority shall be included as conditions of its 

NPDES permits.” EPA carefully considered the suggested language and decided to address this 

suggestion by adding the words “and requirements” after limitations in section 131.14(c) to ensure that 

the terms and conditions of a WQS variance (including any BMPs) are included in the implementing 

NPDES permit. See response Essay 8.g.v for a discussion of cost-effective and reasonable BMPs related 

to nonpoint sources (NPS) and WQS variances.

D. Variances Unrelated to Point Source Discharges

A commenter said: “it is not clear why variances would need to be included as part of an NPDES permit if 

the variance was solely related to non-point source discharges or other reasons unrelated to point source 

discharges. These additional interim requirements should be removed and the NPDES permit 

requirements should just be required to be consistent with the variance while it is in place.” EPA believes 

the commenter mistakenly interprets a WQS variance to a water body or waterbody segment as applying 

only to NPS of pollutants. The main function of a WQS variance is to establish a time-limited WQS 

reflecting the HAC. EPA intends to provide states and authorized tribes the option of adopting a WQS 

variance for a water body or waterbody segment as an alternative to a designated use change in situations 

where the designated use and criterion currently in place for a specific pollutant is not attainable and there 

is uncertainty if and when the water body or waterbody segment will be able to attain the WQS. In such an 

instance, the variance applies to the water body itself, rather than to any specific source or sources. In the 

case of a WQS variance to a water body or waterbody segment, the time-limited WQS applies to all 

dischargers on the water body or waterbody segment. Although NPS are not regulated by NPDES permits, 

EPA considers a WQS variance to a water body or waterbody segment will provide time for the state or 

authorized tribe to work with both point and NPS to determine and implement adaptive management 

approaches on a waterbody/watershed scale to achieve pollutant reductions and strive toward attaining 

the designated use and associated criteria. Although EPA recognizes that situations where a pollutant is

exclusively from NPS are unlikely to benefit from a WQS variance (because NPS are not regulated by 

NPDES permits), EPA sees no need to specifically preclude such a scenario in the final rule. 

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Essay 8.i – Variances: Renewing Variances

A. Long-Term Challenges Will Need Longer than Ten Years: EPA Should Clarify 

That Variances Can Be Renewed

Commenters said that given the maximum term of a water quality standards (WQS) variance is ten 

years, the U.S. Environmental Protection Agency (EPA) should clarify that a WQS variance can be 

renewed because some water quality challenges will require longer than ten years to address. EPA 

acknowledges there may be some circumstances where a WQS variance longer than ten years may be 

needed to address certain long-term water quality challenges. Although the EPA specifically provided for 

WQS variance renewals in the proposed rule at section 131.14(d), some commenters interpreted EPA’s 

maximum WQS variance term of ten years to mean that a discharger may utilize a WQS variance for no 

more than a total of ten years.

As discussed in section II.E of the preamble to the final rule, to address these and other concerns, the 

final rule does not specify a maximum WQS variance term. Instead, the final rule requires states and 

authorized tribes to specify the term of any WQS variance term and provide that it is adequately 

justified in the supporting documentation that must be submitted to EPA with the WQS variance for 

review and approval or disapproval. Thus, where justified, a state or authorized tribe is not limited to 

ten years for any one WQS variance term, and can tailor the WQS variance term to the water quality 

challenge that is being addressed. Furthermore, the preamble of the final rule recognizes that states and 

authorized tribes may adopt a subsequent WQS variance(s) if, at the end of the WQS variance term, the 

underlying designated use remains unattainable. The regulatory text also specifies that a state or 

authorized tribe may adopt a subsequent WQS variance consistent section 131.14. See section 

131.14(b)(1)(iv). EPA also removed from the final rule subsection (d) of the proposed rule addressing 

WQS variance “renewals.” EPA decided a separate subsection was not necessary. The reference to 

adopting a subsequent WQS variance was instead included in other subsections of the section 131.14.

Finally, because the term “renewal” caused confusion, the final rule uses the words “adopt a 

subsequent variance.” 

Commenters also suggested that EPA allow alternative ways to express the term of a WQS variance 

other than specific expiration date. EPA agrees with these commenters. Consequently, in the final rule, 

the EPA is retaining the concept of requiring states and tribes to identify a definite term for the WQS 

variance, but no longer identifies it as the “expiration date.” States and authorized tribes may articulate 

the term of a WQS variance by either specifying an interval of time with respect to EPA approval of the 

WQS variance, or a specific date that is as short as possible and is consistent with the demonstration 

provided in section 131.14(b)(2). See also response Essay 8.g.iii for more discussion on the expiration 

date topic.

B. A Water Quality Standards Renewal Should Not Be Treated as a Water 

Quality Standards Action

Commenters said: “the renewal should not be treated as a standards action except to the extent the 

extension requires modification of an existing variance policy.” Commenters also claim that approval of 

a WQS variance renewal “removes the power and discretion currently held by states and tribes, and 

transfers it to the EPA.” 

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EPA disagrees with these commenters. A WQS variance has always been and continues to remain a WQS

subject to EPA action under Clean Water Act (CWA) section 303(c) (see response Essay 8.f.i). Thus states 

and authorized tribes must submit WQS variances to EPA for review and approval or disapproval. The 

final rule defines a WQS variance in section 131.3(o) as “a time-limited designated use and criterion for a 

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

the term of the WQS variance.” To ensure the WQS variance is time limited, the final rule requires the 

WQS variance must have a defined term after which it is no longer the applicable WQS. States and 

authorized tribes may adopt a subsequent WQS variance if the WQS variance is consistent with 

section 131.14. However, the subsequent “renewal” WQS variance is a new WQS action under CWA 

section 303(c) and requires EPA review and approval or disapproval. EPA’s action in reviewing and 

approving a WQS variance is EPA carrying out its CWA oversight authority as it does with all new and 

revised WQS. It is not transferring any power to EPA that is currently held by the states. States have full 

discretion to decide whether to adopt a WQS variance. See also section II.E of the preamble to the final 

rule which discusses several ways that states and authorized tribes may be able to streamline the 

adoption of (including adoption of subsequent) WQS variances.

C. Suggested Regulatory Text Revisions 

Commenters suggested deleting proposed section 131.14(d) and replacing it with only “(d) WQS 

variance renewals: The State must document whether and to what extent BMPs have been 

implemented to address the pollutant(s) subject to the WQS variance and the water quality progress 

achieved during the WQS variance period.” As discussed above, EPA decided not to include the 

proposed subsection (d) in the final rule. The final rule includes a provision that a state or authorized 

tribe may adopt a subsequent WQS variance at the end of the WQS variance term. Any subsequent WQS 

variance would need to comply with section 131.14. To the extent the commenter wanted there to be 

no requirements regarding adoption of a subsequent WQS variance, EPA disagrees. It is important that 

any subsequent WQS variance meet the same requirements as for an initial WQS variance. The 

requirements in section 131.14 are designed to ensure that progress is made in improving water quality 

with the goal being to ultimately attain the underlying WQS. To remove any requirements related to 

adopting subsequent WQS variances would undermine that objective and goal. EPA did retain the 

language from subsection (d) of the proposed rule that the commenters suggested be retained. It 

appears in section 131.14(b)(2)(iii)(B).

Commenters suggested revising the proposed rule at section 131.14(d) to: “A variance may be renewed 

subject to the demonstration under (b)(2) above [demonstration that attaining WQS not feasible 

because of one of the § 131.10(g) factors in rule].” For the reasons discussed above, EPA considers that 

all the requirements important to justifying an initial WQS variance remain equally important to 

justifying adoption of a subsequent WQS variance.

The commenters suggest a variety of revisions to section 131.14 specifying that only WQS variance 

policies and procedures, not individual WQS variances, are WQS subject to EPA review and approval or 

disapproval. Other suggested revisions provide full state discretion over all aspects of WQS variances 

(e.g., WQS term and determination of the highest attainable use [HAU]). For reasons discussed in the 

preamble and in other responses to comments (for example, see response Essays 8.f.i and 8.g.iii), EPA 

has determined that it is necessary and appropriate to review each individual variance for its 

concordance with the provisions in the final rule to properly fulfill the oversight role provided in the 

CWA. 

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D. Unless States Regulate Nonpoint Sources, There Is No Way to Identify and 

Document Best Management Practices 

See response Essay 8.g.v for discussion about nonpoint sources (NPS), including best management 

practices (BMPs) for NPS. 

E. When Could a Subsequent Water Quality Standards Variance Be 

Disapproved? 

Commenters said: “How would ‘feasible progress’ be defined, and would progress be determined by the 

states or EPA? Would ‘feasible progress’ have to include NPS controls, as implied in the rule? If progress 

was unable to be achieved due to conditions beyond the reasonable control of the permittee - such as 

technological, regulatory, or other limitations - would a discharger lose the variance?” 

Commenters are referring to the following statement in the preamble to the proposed rule discussing 

when a renewal of WQS variances might be appropriate: “If a variance term will expire and the applicant 

complied with the conditions of the original variance (e.g., feasible progress has been made), but the 

designated use and criterion remain unattainable, then renewal of a variance may be an appropriate 

action for the state or tribe to consider.” As discussed above, EPA is not promulgating subsection (d) in 

the final rule, which this statement was addressing. The final rule does include a provision recognizing 

that states and authorized tribes may adopt subsequent WQS variances if those variances satisfy the 

requirements of section 131.14. EPA believes that such an adoption process will bring forth the 

necessary information and considerations to inform whether a subsequent WQS variance has been 

justified. The language to which comment relates is not in the rule or preamble to the final rule. In 

addition, as discussed in section II.E of the preamble to the final rule, EPA has added several provisions 

to increase the accountability in the use of WQS variances in order to ensure that progress toward the 

underlying WQS is made during the term of the WQS variance. Commenters said in the context of 

renewing a WQS variance: “EPA should clarify that any conditions in a WQS variance be limited to the 

alternative criteria a permittee must meet.” Commenters also want “clarification, or examples, of when 

circumstances out of the permittee’s, state’s, or tribe’s control would lead to denial of a variance.” 

The final rule does not include any special conditions related to adoption of a subsequent dischargerspecific variance other than such variance must be consistent with section 131.14. Each WQS variance 

will need to be supported and reviewed on a case-by-case basis. In regards to a WQS variance applicable 

to a water body or waterbody segment, the final rule includes a provision at section 131.14(b)(2)(iii)(B) 

which states that “Any subsequent WQS variance for a water body or waterbody segment must include 

documentation of whether and to what extent best management practices for nonpoint source controls 

were implemented to address the pollutant(s) or water quality parameter(s) subject to the WQS 

variance and the water quality progress achieved.” This is same as the proposed requirement for 

renewal of water body variances, with the exception that, as noted earlier in this essay, EPA moved 

away from the term “renewal” due to the confusion it created. EPA continues to consider this 

requirement reasonable and important for this particular class of WQS variances. This provision does 

not require implementation of BMPs for NPS. Instead it ensures that EPA and public have the 

information about the consideration and implementation of BMPs for NPS needed to consider a 

subsequent WQS variance applicable to a water body or waterbody segment and ensure that the tool is 

used to make progress toward the underlying WQS and not retain the “status quo.” As a reminder, this 

type of WQS variance is only likely to be used where the state or authorized tribe has brought point and 

NPS (and other stakeholders) to the table in a joint effort to move a difficult water quality challenge 

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forward and where much of that progress is dependent on mitigation of the NPS of the particular 

pollutant(s) that are the subject of the WQS variance.

When a WQS variance expires, the state or authorized tribe can determine the appropriate mechanism 

to continue making progress toward the underlying designated use and criterion, which may include 

adoption of a subsequent WQS variance (which must also be consistent with section 131.14). Like the 

original WQS variance, a subsequent WQS variance is itself a WQS subject to EPA review and approval or 

disapproval. EPA acknowledges that a WQS variance can be potentially utilized in a wide variety of 

circumstances. EPA believes it would not be helpful nor appropriate to speculate on case-specific 

hypothetical scenarios described by commenters in a national rule. EPA encourages states, authorized 

tribes, stakeholders, and the public to refer to EPA guidance, or contact their regional EPA offices for 

case-specific assistance. 

F. Relationship between Water Quality Standards Variance and National 

Pollutant Discharge Elimination System Permit Terms

Commenters suggested: “EPA [should] add an administrative continuance mechanism similar to the one 

for expiring, administratively continued NPDES permits under 40 CFR §122.6. As long as a renewal 

application is timely and complete, then the discharger should continue to enjoy the protections of the 

variance pending agency action on the renewal application.” 

EPA does not agree that a WQS variance should be administratively extended based on the filing of a 

timely request for adoption of a subsequent WQS variance. Such a provision could defeat the purpose of 

having a term for each WQS variance. The mere filing of a request for adoption of a subsequent WQS 

variance should not automatically extend the original WQS variance pending a state decision whether to 

adopt a subsequent WQS variance and EPA’s approval. A WQS variance will expire at the end of its term.

The state or authorized tribe may adopt a subsequent WQS variance but the original WQS variance does 

not remain in effect after its term ends. Importantly, because the end date of the original WQS variance 

will be clear (to meet the requirements of the final rule), and for longer-term WQS variances there will 

have been thorough reevaluations at regular intervals, a state or authorized tribe can easily anticipate 

the need for a subsequent WQS variance with enough time to adopt and receive EPA action on the 

subsequent WQS variance before the original WQS variance comes to an end.

That said, EPA agrees that if a discharger has a National Pollutant Discharge Elimination System (NPDES( 

permit that includes a water quality-based effluent limit (WQBEL) based on a WQS variance whose term 

runs to the end of the permit term, that the WQBEL based on the WQS variance would be 

administratively continued if the permit is administratively continued. A specific provision in 

section 131.14 is not necessary for an administratively extended NPDES permit to continue to provide 

the permittee with a shield until the permit is reissued. See response essay 8.f.ii for more information 

on the relationship between WQS variance and NPDES permit terms. 

Commenters said: “It also would be appropriate for a variance, implemented through a permit, to have 

an end date coincident with the expiration of that permit rather than a specific variance term.” EPA does 

not think it is necessary or appropriate to require WQS variance terms to have the same expiration date 

as the relevant NPDES permits. EPA has explained its position regarding the terms for variances in 

response Essay 8.g.iii. States and authorized tribes have the discretion to align as best they can the term 

of a WQS variance with the term of an NPDES permit. See EPA’s discussion in section II.E of the

preamble to the final rule and response essay 8.g.iii for a discussion of reevaluation requirements. 

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G. Support

EPA appreciates the time and effort to provide comments on the renewal provision.

H. Most Water Quality Standards Variances Should Not Be Renewed, and If so, 

Rarely and with Scrutiny

Commenters said: “there are very few legitimate circumstances under which a variance should be 

renewed. There are far too many examples whereby permitted facilities receive approvals for multiple 

variance renewals, spanning decades of noncompliance, essentially resulting in unpromulgated sitespecific WQS that are not and never will be protective of water resources.” Commenters also said: “The 

renewal process must explicitly include a requirement for a clear showing of need for the renewal and a 

public review process “ and “EPA provides that the variances can be renewed, largely indefinitely, even 

in the face of continued variance noncompliance.” 

EPA acknowledges commenters’ concerns about ensuring WQS variances are utilized appropriately and 

that subsequent WQS variances are not issued unless justified. The final rule includes detailed and 

protective submission and documentation requirements designed to avoid the concerns raised by the 

commenters. Commenters’ concerns would reflect the WQS variance process prior to EPA’s new rule. 

EPA is adopting its new rule in part to bring greater uniformity, accountability, transparency and scrutiny 

to the WQS variance process. See comment response essays 8.b, 8.d, and 8.f.i for discussion on 

provisions in the final rule to ensure transparency and accountability in the use of WQS variances.

Commenters said: “a maximum single variance term of no more than 10 years, as proposed, should also 

be the only term. There should be no extensions. If a variance cannot be corrected to comply with water

quality conditions within 10 years other options need to be sought.” 

EPA carefully considered the comments but for the reasons discussed elsewhere in the preamble and 

response to comments decided that there should not be a fixed maximum term in the regulation. Those 

reasons also apply to why adoption of a subsequent WQS variance should not be prohibited. Although 

EPA expects most WQS variances to be relatively short, there are some circumstances that require longterm efforts, either in the term of the original WQS variance or as justification for adoption of a 

subsequent WQS variance. For example, states and authorized tribes are beginning to develop and 

implement numeric criteria for nitrogen and/or phosphorus which are the cause of harmful algal blooms

and other eutrophication-related problems. There are many common sources of nitrogen and 

phosphorus that have existed for many years, and restoration plans for some effected waters may

require relatively long time horizons. EPA believes providing a WQS tool that allows states and 

authorized tribes in such circumstances to incrementally reduce nitrogen and/or phosphorus loads to 

the greatest extent possible is preferable to the state or authorized tribe permanently downgrading or 

removing the designated use. 

EPA acknowledges commenters concerns that long-term WQS variances or adoption of subsequent WQS 

variances could be used inappropriately. To address these concerns, the final rule specifies that the term 

of a WQS variance shall only be as long as necessary to achieve the highest attainable condition (HAC). 

To ensure EPA has sufficient information to determine whether the WQS variance is only as long as 

necessary, states and authorized tribes must provide documentation to justify why the WQS variance is 

needed, the term for the WQS variance, and the HAC. To ensure that a WQS variance longer than five 

years reflects the HAC throughout the WQS variance term, states and authorized tribes must reevaluate 

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the WQS variance at least every five years, and adopt a provision specifying that the applicable interim 

WQS shall be either the HAC initially adopted, or a higher attainable condition later identified during any 

reevaluation. The final rule specifies that this provision must be self-implementing so that if any 

reevaluation yields a more stringent attainable condition, that condition becomes the applicable interim 

WQS without additional action. These provisions in the final rule will ensure that long-term WQS 

variances are used appropriately.

I. Best Management Practice Requirements Add Complexity, Have No Purpose, 

and Are an Unnecessary Burden

Commenters said the rule would “significantly amend existing requirements in ways that go beyond 

existing law or understandings, with no apparent purpose other than to add complexity and burdens” 

such as: “Requiring that the state provide documentation as to the extent to which BMPs have been 

imposed on nonpoint sources in the area as a prerequisite to renewal of variances (131.14(d)).” 

EPA disagrees with these commenters regarding the purpose of these new requirements. A WQS 

variance applicable to a water body or waterbody segment provides the state or authorized tribe with 

an alternative to permanently downgrading or removing the designated use. Receiving waters with

multiple sources of pollutants (both point and nonpoint) require a holistic approach to achieve the 

pollutant reductions needed to attain the designated use. A WQS variance applicable to a water body or 

waterbody segment provides time for states and authorized tribes to work with both point and NPS to 

determine and implement adaptive management approaches on a waterbody/watershed scale. The 

requirement that states and authorized tribes identify and document any cost-effective and reasonable 

BMPs for NPS controls ensures the public understands the role NPS play in the water body or waterbody 

segment, and is an important first step for addressing complex water quality issues involving both point 

and NPS. 

Commenters said the rule: “requires documentation for any subsequent renewals that includes 

‘whether and to what extent BMPs have been implemented to address the pollutant(s) subject to the 

water quality standard (WQS) variance and the water quality progress achieved during the WQS 

variance period’”. Commenters assert that this will establish a significant burden on permittees to 

generate proof for a regulatory standard that is not adequately defined and likely to be interpreted 

inconsistently across EPA regions.

EPA disagrees with these commenters. The purpose of a WQS variance is to make progress toward the 

designated use with the ultimate goal of use attainment. EPA notes that the provision in question is only 

required for WQS variances applicable to a water body or waterbody segment and is not required for 

single or multiple discharger WQS variances. As described above, when adopting a WQS variance 

applicable to a water body or waterbody segment, it is important for states and authorized tribes to 

consider all pollutant sources that contribute to nonattainment.

J. Grandfathering Existing Water Quality Standards Variances and Variance 

Practices

“It is important for the rule also to explain how the new requirements would apply to renewals of 

variances that initially were issued prior to the effective date of the rules. In this regard, the rule clearly 

should state that such renewals similarly would not be subject to the new requirements. In light of how 

far down the road MassDEP, MWRA and EPA Region 1 are with the MWRA variance program, to change 

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the applicable requirements now would be counterproductive at best. MassDEP, accordingly, at 

minimum urges EPA to exempt such renewals from the new requirements.” 

States and authorized tribes must meet the requirements of this rule on the effective date of the rule. 

See sections I.E and II.E of the preamble to the final rule for more information on the effective date for 

the final rule. EPA has heard from states, tribes, and stakeholders that there is confusion, inconsistency, 

and mixed interpretations about how, when, and where variances may be used appropriately. This final 

rule is intended to provide specificity and national consistency in how states and authorized tribes utilize 

WQS variances.

It is important that going forward all WQS variances be adopted and reviewed under the same rules in 

order to provide the consistency and protectiveness intended by the new rule. EPA has decided that the 

new rule should also apply to adoption of a subsequent WQS variance when the original WQS variance 

was adopted prior to the final rule. Allowing adoption of subsequent WQS variances without applying 

the new rule could allow the indefinite continuation of the adoption of WQS variances that do not meet 

the new protections merely because an original WQS variance was issued prior to the new rule. States 

and authorized tribes will have time to adapt and respond to the requirements of the new rule. EPA will 

also work closely with states, authorized tribes and the public with the transition to the new rule. EPA 

has included provisions to allow WQS variances that were adopted before the new rule to continue until 

their term expires. In regard to the specific situation highlighted by MassDEP, EPA notes that this is a 

state specific case and EPA will work directly with the state of Massachusetts to determine how the new 

requirements will affect subsequent WQS variances that are part of the MWRA variance program based 

on the framework that EPA initially approved.

K. Nonpoint Source Best Management Practices Requirements Too Weak

A commenter suggested the following revision to proposed section 131.10(d) to include documentation 

whether identified BMPs were implemented as a basis for EPA approval of a variance renewal: “(d) WQS 

variance renewals: EPA may approve a WQS variance renewal if the State meets the requirements of 

this section and provides documentation of the actions taken to meet the requirements of the previous 

WQS variance, [begin new text] including [end new text] [begin strikeout]. For a waterbody WQS 

variance renewal, the state must also provide [end strikeout] documentation of whether and to what 

extent BMPs [begin new text] identified in paragraph (b)(3) [end new text] have been implemented to 

address the pollutant(s) subject to the WQS variance and the water quality progress achieved during the 

WQS variance period. Renewal of a WQS variance may be disapproved if the applicant [begin new text] 

or state [end new text] did not comply with the conditions of the original WQS variance, or otherwise 

does not meet the requirements of this section.” 

EPA agrees with the intent of one suggested revision and incorporated its intent into a reorganization of 

the rule text. The commenters suggested adding “or state” with the intention of ensuring accountability 

for any state or authorized tribal responsibilities that are part of a WQS variance. Section 

131.14(b)(2)(iii)(B) of the final rule says: “Any subsequent WQS variance for a water body or waterbody 

segment must include documentation of whether and to what extent best management practices for 

nonpoint source controls were implemented to address the pollutant(s) or water quality parameter(s) 

subject to the WQS variance and the water quality progress achieved.” This revised language does not 

limit responsibility to only the “applicant.” 

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EPA disagrees with the intent of several of the suggested revisions. The suggested revisions add the 

documentation requirement for NPS controls to all WQS variances. See comment response essay 8.g.v 

for discussion of why the final rule does not require documentation of NPS controls for dischargerspecific WQS variances.

Commenters also suggested revisions to the rule text that specifies the NPS controls requiring 

documentation are those specified in the WQS variance. EPA disagrees with these commenters. In 

today’s final rule, the requirement to identify and document any cost-effective and reasonable BMPs for 

NPS controls is limited to WQS variances that apply to a water body or waterbody segment. States and 

authorized tribes are not required to identify specific NPS in their WQS variance because the WQS 

variance is applicable to a specific water body and not a specific source. Therefore, it would not be 

consistent with the intent of the provision to limit the identification and documentation of NPS to those 

specified in the WQS variance as it could be a null set. As discussed in the preamble to the proposed 

rule, “Because other sources of pollution (e.g., nonpoint sources) can have a significant bearing on 

whether the designated use and associated criteria for the entire water body are attainable, it is 

essential for states and tribes to consider and provide information to the public regarding the impact of

controlling other sources through application of cost-effective and reasonable BMPs could have on 

water quality before granting a waterbody variance.” In regards to the final rule requirement that states 

and authorized tribes must document whether and to what extent BMPs for NPS were implemented to 

address the pollutant(s)/parameters(s) subject to the WQS variance, it would be inappropriate and 

incomplete to limit such documentation to just those that were identified and documented when the 

WQS variance was initially adopted. EPA expects that over the course of a WQS variance, states and 

authorized tribes and their stakeholders may discover other effective BMPs to control NPS than were 

identified and documented at the onset and limiting would again be contrary to the intent of the 

provision. For example, where a WQS variance applicable to a water body or waterbody segment has a 

duration longer than five years, it is likely that the state or authorized tribe or the public may identify 

additional BMPs during the required reevaluations which would result in a “higher” attainable condition 

for the water body. 

Finally, commenters said the rule should require NPS BMPs to the extent possible as a condition of a 

WQS variance renewal, and if the rule does not require implementation of NPS BMPs as a condition of 

renewal, they will never happen. EPA believes that the requirements in the final rule strike the correct 

balance between bringing information regarding BMPs for NPS controls into the process when 

considering whether to adopt a WQS variance and what conditions to include in the WQS variance. 

However, in the context of a WQS variance applicable to a water body or water body segment, decisions 

regarding NPS controls can present complex and complicated challenges involving many parties. EPA 

concluded it was most appropriate to include the requirement to identify and document BMPs for 

consideration during the WQS variance adoption process. But EPA concluded that requiring 

implementation of BMPs for NPSs as a condition of adopting a WQS variance could make states and 

authorized tribes reluctant to pursue a WQS variance applicable to a water body or waterbody segment.

In addition, it might lead to states and authorized tribes selecting a very limited or restricted list of BMPs 

therefore missing the opportunity to look more broadly and engage a larger group of stakeholders. See 

also response essay 8.g.v. for additional discussion of BMPs for NPS.

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Essay 8.i.i – Variances: NPS Requirements for Renewing Water Body

Variances 

No comments are assigned to this issue category, and thus no response is necessary.

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Essay 8.j – Variances: EPA Promulgated Designated Uses

A. General

The U.S. Environmental Protection Agency (EPA) acknowledges the commenters noting that the federal 

promulgations at sections 131.34 and 131.40 do not affect waters under their jurisdictions. EPA agrees 

that sections 131.34 and 131.40 only apply to waters in Kansas and Puerto Rico, and thus the final rule 

revisions at section 131.34(c) and section 131.40(c) do not apply to waters in Wisconsin or the Pueblo of 

Sandia.

With regard to the commenter requesting that EPA initiate a withdrawal of the federal promulgation for 

Kansas at section 131.34 instead of finalizing the revision to section 131.34(c), EPA disagrees. Neither 

the proposed rule nor the final rule contemplated withdrawing the federal promulgation for Kansas at 

section 131.34. In the future, EPA may evaluate whether the federal water quality standards (WQS) 

established at section 131.34 continue to be necessary to meet the requirements of the Act. If EPA 

determines that the federal WQS are no longer necessary and Kansas’ EPA-approved WQS meet the 

requirements of the Act, EPA would initiate a rulemaking to withdraw the federally promulgated WQS. 

Regardless of whether EPA withdraws the federal WQS at section 131.34, WQS variances for waters in 

Kansas will be governed by the final requirements at section 131.14. This is because the final rule 

deletes the previous specific variance procedures from section 131.34(c) and instead requires WQS 

variances for waters covered by section 131.14 to be consistent with the final requirements at section 

131.14. Similarly, if EPA withdraws section 131.34, WQS variances must be consistent with the nationally 

applicable final requirements at section 131.14.

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Essay 8.k – Variance: Linkages with Great Lakes Initiative

A. General

Commenters requested that the U.S. Environmental Protection Agency (EPA) change Title 40 of the Code 

of Federal Regulations (CFR) Part 132 in order to prevent creating overlapping water quality standards 

(WQS) variance requirements for states and tribes in the Great Lakes. For waters in the Great Lakes 

basin, states and authorized tribes must meet the requirements of both 40 CFR Part 131 (the WQS 

regulation) and 40 CFR Part 132 (the Great Lakes Initiative [GLI] or Great Lakes Water Quality Guidance

[GLWQG]). See 40 CFR 131.5(a)(5).

EPA promulgated the Part 132 regulations pursuant to congressional directive in Clean Water Act (CWA) 

section 118. The Part 132 rule is a comprehensive rule that includes requirements addressing both 

adoption of WQS and issuance of National Pollutant Discharge Elimination System (NPDES) permits. It 

includes requirements unique to the Great Lakes basin waters reflecting the requirement in section 118 

that the Great Lakes rule “conform with the objectives and provisions of the Great Lakes Water Quality 

Agreement.” Section 118(c)(2)(A). EPA’s current rulemaking was never intended to make any revisions 

to the Part 132 regulations. To the extent there are overlapping requirements for variances under Parts 

131 and 132, EPA also does not anticipate any undue complications. The commenter did not identify any 

specific issues of concern. Where regulations in 40 CFR Parts 131 and 132 overlap, the more stringent 

regulation applies. EPA understands that in some situations determining which provisions are “more 

stringent” may be complex. EPA will consider this topic as it develops future guidance.

In some cases, the flexibilities and requirements in the national rule will not be applicable to waters in 

the Great Lakes basin. For example, the GLWQG limits any WQS variance to a maximum term of five 

years (with the ability to obtain a subsequent WQS variance). Therefore, any WQS variance on waters 

that are subject to the GLWQG cannot exceed five years even though today’s final rule in 40 CFR Part 

131 does not specify a maximum term. On the other hand, because GLWQG WQS variances cannot 

exceed five years, the requirements in the final rule at section 131.14 that pertain to conducting 

reevaluations (for WQS variances greater than five years) are not applicable.

One commenter compared several aspects of the WQS variance requirements at 40 CFR Part 132, 

Appendix F, Procedure 2 with the requirements of EPA’s proposed rule and stated that EPA’s rule does 

not contain a number of provisions that are in Part 132 that the commenter found to provide important 

protections. One example cited by the commenter is the provision in Part 132 that variances may not 

exceed a term of five years. EPA acknowledges that the final rule does not include all of the provisions in 

the Part 132 variance rule. EPA did carefully consider the Part 132 rule in developing the WQS variance 

requirements in section 131.14 and the final rule does reflect some of the provisions in the Part 132 

variance rule. While section 131.14 does not include all of the provisions from the Part 132 variance 

rule, EPA believes the final rule provides a comprehensive and protective WQS variance program. See 

also response Essay 8.g.iii for a discussion of the duration of a WQS variance.

The commenter noted that the requirements in 40 CFR Part 132 explicitly require variances to be reviewed 

triennially. EPA notes that the final rule makes clear that a WQS variance is a WQS subject to EPA’s review 

and approval or disapproval. EPA’s final rule also makes clear in section 131.20(a) that states and 

authorized tribes must review all “applicable” WQS adopted pursuant to sections 131.10–131.15 and 

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federally promulgated WQS, which includes WQS variances. The commenter also noted that 40 CFR Part 

132 ensures that a renewal of a WQS variance is subject to the same findings and procedures as the 

original variance. EPA’s final rule contains a provision at section 131.4(b)(1)(iv) that allows states and 

authorized tribes to adopt subsequent WQS variances as long as they are consistent with the regulations 

at section 131.14. Additionally, since EPA’s final rule no longer includes a maximum WQS variance 

duration of 10 years (when a state or authorized tribe can justify a longer term), there may potentially 

be less need for a state or authorized tribe to renew a WQS variance (or at least to renew a WQS 

variance as frequently). The comments note that the variance requirements at 40 CFR Part 132 require 

reasonable progress toward attaining WQS. EPA’s final rule at section 131.14 outlines a regulatory 

framework for states and authorized tribes to establish interim requirements that reflect the highest 

attainable condition (HAC) during the term of the WQS variance that apply for purposes of CWA section 

402 permitting and in issuing certifications under CWA section 401 and provides states and authorized 

tribes with time to implement adaptive management approaches that drive progress towards meeting 

the designated use and criterion. The commenter noted that the WQS variance at 40 CFR Part 132 

includes a clear prohibition against the use of WQS variances for new or recommencing dischargers. 

EPA’s final rule does not prohibit new or recommencing dischargers from utilizing a WQS variances, 

however, EPA’s final rule does not allow a WQS variance to lower currently attained ambient water 

quality, except in circumstances where a WQS variance will allow short-term lowering necessary for 

restoration activities consistent with section 131.14(b)(2)(i)(A)(2). See also response Essay 8.f.i for a 

discussion regarding new dischargers.

B. Other

With regard to the comments related to the maximum timeframe, see EPA’s response to code 8.g.iii.

With regard to the comments related to the use of waterbody variances, see EPA’s response to code 

8.f.i.

With regard to the commenter noting that 40 CFR Part 132 includes antidegradation requirements, see 

EPA’s response to code 7.k.

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Essay 8.l – Variances: General Comments

A. The Rule Should Establish a “Rebuttable Presumption” to Obtain a Water 

Quality Standards Variance Renewal

Commenters said: “the EPA [should] establish a rebuttal presumption that a variance is no longer 

justified upon the expiration of the first period granting the variance, to ensure that during the time 

period reasonable (not feasible) progress is being made toward the designated use. The presumption 

can be rebutted to request an extension only if it satisfies all of the three steps above. Specifically, to 

rebut the presumption, it has to be established that conditions have not changed so that the designated 

use or criterion are now attainable (and not due to the fault of the party being granted the variance), no 

new or additional information is available to indicate that the designated use and criterion are not 

attainable in the future, and that reasonable progress is being made toward the designated use and 

criterion and that additional time is needed to make further reasonable progress.” 

Although the term “rebuttable presumption” is not explicitly used in the context of water quality 

standards (WQS) variances, the final rule accomplishes the same objective. The final rule provides that a 

state or authorized tribe may only adopt a WQS variance if it is consistent with section 131.14. 

Section 131.14 specifies that the requirements that apply during the term of the WQS variance must be

the highest attainable condition (HAC) and it requires states and authorized tribes to submit 

documentation affirming such a determination. If the HAC is not the underlying designated use, then by 

definition, the underlying designated use and criterion is not attainable. Requiring the state or 

authorized tribe to demonstrate that the underlying designated use is not attainable in order to obtain a 

WQS variance assumes the underlying designated use is attainable unless the state or authorized can 

demonstrate otherwise. 

The U.S. Environmental Protection Agency (EPA) disagrees with commenters that said the rule should 

specify that EPA will approve a subsequent WQS variance only if “no new or additional information is 

available to indicate that the designated use and criterion are not attainable in the future.” One of the 

stated goals of section 131.14 is to explicitly authorize the use a WQS variance to make progress toward 

a designated use when the designated use is not attainable in the near-term but may be attainable in 

the future. 

EPA removed the regulatory language saying: “Renewal of a WQS variance may be disapproved if the 

applicant did not comply with the conditions of the original WQS variance” because EPA eliminated the 

proposed ten-year maximum WQS variance term and instead requires reevaluations of WQS variances 

longer than five years no less frequently than every five years and allows for subsequent WQS variances 

if they are consistent with section 131.14. In the final rule, states and authorized tribes have the 

responsibility of specifying and justifying the term of the WQS variance and the responsibility to conduct

ongoing scrutiny of the WQS variance through regularly scheduled reevaluations. The final rule requires 

the term of any WQS variance to be no longer than necessary to achieve the HAC. To ensure that a WQS 

variance reflects the HAC throughout the WQS variance term, states and authorized tribes must also 

adopt a provision specifying that the requirements that apply during the term of the WQS variance shall 

be either the HAC initially adopted, or a higher attainable condition later identified during any 

reevaluation. This provision must be self-implementing so that if any reevaluation yields a more 

stringent attainable condition, that condition becomes the applicable WQS (for the purposes of 

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developing National Pollutant Discharge Elimination System (NPDES) limitations and requirements or for 

issuing 401 certifications) without additional action. Where a “higher” attainable condition has been 

identified during a reevaluation, the permitting authority, upon permit reissuance, will base the water 

quality-based effluent limit (WQBEL) on this more stringent applicable WQS consistent with the NPDES 

permit regulation at section 122.44(d)(vii)(A). The final rule also requires states and authorized tribes to 

obtain public input on the reevaluations and submit the results of the reevaluations to EPA. EPA 

concluded that the combination of provisions in the final rule provide a framework for WQS variances 

that will allow states and authorized tribes to efficiently address long-term water quality challenges

while ensuring that states and authorized tribes remain accountable for utilizing WQS variances 

appropriately.

B. EPA Should Provide Guidance on How to Utilize Water Quality Standards

Variances

Commenters said EPA should: “provide guidance on what types of requests would be granted, what 

information would be required, and if EPA were to offer some assurance that the process would be 

reviewed differently than it has been in the past.” 

EPA is establishing section 131.14 in part to encourage states and authorized tribes to utilize WQS 

variances to make progress toward WQS that are not currently attainable but may be attainable in the 

future. To this end, EPA wants states and authorized tribes to succeed in utilizing WQS variances 

effectively. EPA expects states and authorized tribes to utilize WQS variances in a wide variety of 

circumstances, and will update its guidance as the need arises.

C. Other

Commenters said: “We are concerned that the proposed regulations will discourage, not encourage 

variances, contrary to EPA’s stated goal. We recommend addressing variances with more flexibility than 

EPA has proposed, and doing so in guidance rather than by regulation, to ensure water quality standards 

implementation decisions are left with States.” Other commenters said: “EPA proposes to add a new 

section to the WQS Regulation to regulate State adoption of variances. As a threshold matter, variances 

should be addressed in guidance rather than regulation, to ensure WQS implementation decisions are 

left with States and Tribes. Guidance could encourage the issuance of variances in certain situations 

when requested by the permittee, and provide basic elements of how variances should be issued, 

without mandating specifics. States and Tribes should be allowed to dictate specifics for themselves.” 

EPA determined it would be most effective in promoting the use of WQS variances and ensuring those 

WQS variances are protective to have consistent national regulations. EPA’s experience with the use of 

variances under the Great Lakes rule supports that position. See response essay 8.b and 8.f.i. See also 

response essay 8.m regarding the issue of state primacy in regards to WQS variances. 

Commenters said: “The State of Colorado has been successfully implementing temporary modifications 

and ambient-based criteria for many years. These are two alternatives to variances or permanent use 

downgrades that were recognized in EPA’s Advance Notice of Proposed Rulemaking, 63 FR 36742 (July 7, 

1998). The Proposed Rule does not include clarifications regarding either temporary modifications or 

ambient-based criteria. Pueblo supports EPA’s decision not to include temporary modifications or 

ambient based criteria, since clarification of these regulatory options is not necessary to facilitate their 

continued use.” To be approved as a Clean Water Act (CWA) WQS variance, the variance would need to 

be consistent with the requirements of the final rule at section 131.14. See response essay 8.a.

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Commenters said: “Clarify that conditional discharge prohibitions are not variances” and a “conditional 

discharge prohibition is a permitting tool that allows the state to specify the discharge conditions that 

will ensure an authorized discharge meets applicable WQS without the need for a variance to allow a 

limited-term exceedance of such WQS. The preamble accompanying the final rule should clarify this 

point.” 

The NPDES permit regulation at section 122.44(d)(vii)(A) requires the permitting authority to develop 

WQBELs that derive from and comply with all applicable WQS. The final rule establishes WQS variances 

as a regulatory mechanism that allows states and authorized tribes to develop NPDES permits that 

comply with section 122.44(d)(vii)(A) in certain situations where the permittee cannot meet the WQBEL 

for the underlying designated use. The CWA and NPDES regulations continue to govern issuance of 

NPDES permits. This final rule does not address discharge prohibitions See response essays 8.a, 8.b, and 

8.f.i for further discussion of why a WQS variance is a WQS and ways to streamline the process of 

adopting WQS variances into state and authorized tribal WQS.

Commenters said EPA should consider providing guidance on the use of variances to preserve flexibility 

for states to address site-specific issues instead of issuing a regulation. As mentioned above, EPA 

determined it would be most effective in promoting the use of WQS variances and ensuring those WQS 

variances are protective to have consistent national regulations. EPA’s experience with the use of 

variances under the Great Lakes rule supports that position. See also response essay 8.b.

Commenters said: “An option should be available for States to develop a variance rule and to adopt it 

into their State rule with EPA approval. If the variance rule has been approved by EPA, each specific 

variance should not then require EPA approval as long as the variance rule is followed.” See response 

essay 8.b for a general discussion on this issue and for information on EPA’s longstanding practice for 

WQS variances. Also see response essay 8.f.i for a discussion on why WQS variances, themselves, are 

WQS needing review and approval by EPA. 

Commenters said: “Thermal variances are unique variances and should not be included with those that 

are subject to the proposed requirements. We request that language be added to both the preamble 

and the proposed regulations, clarifying that thermal variances issued in accordance with Section 316(a) 

of the CWA are not subject to the proposed rulemaking regarding variance procedures.” The rule does 

not apply to section 316(a) variances. See response essay 8.c.

Commenters said EPA should not promulgate regulations for WQS variances because the previous 1983 

rulemaking said they are not “regulatory in nature.” See response essay 8.b

Commenters request clarification of the review and approval process for WQS variances because the 

rule does not appear to establish clear responsibilities for individual permittees that may wish to obtain 

a variance as the Part 132 regulations does. First, EPA notes that the Part 132 regulation is both a WQS 

and permitting regulation, and therefore, addresses individual permittees directly. The revisions to Part 

131 to add specific requirements for WQS variances is only a WQS regulation. Under section 131.14, EPA 

defers to states and authorized tribes in their implementation of the regulation as long as it is consistent 

with the section 131.14. See also response essays 8.g.iv and 8.k. 

Commenters said: “we strongly encourage EPA to include preamble language stating that currently 

approved state regulatory tools will continue to be valid once the proposed rule is finalized” and suggest 

regulatory language to ensure current state WQS variance policies continue to be valid. See response 

essay 8.b for a discussion on why EPA disagrees with this position as it pertains to WQS variances or 

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variance policies/procedures. Where states and authorized tribes have binding WQS variance policies 

and/or procedures inconsistent with today’s rule, those states and authorized tribes will need to revise 

such policies and/or procedures as necessary to be consistent with the federal regulations if the state or 

authorized tribe wants to continue to adopt WQS variances. This should occur prior to, or 

simultaneously with, adopting the first WQS variance, consistent with the timeframe described in the 

effective date discussion in section I.E of the final preamble. 

Commenters said: “EPA’s proposed changes will lead to permittees wanting to over-utilize this 

approach. In these times of strained resources, it may be challenging for states to respond to these 

increased requests.” Commenters also questions “whether the standards set out in proposed § 131.14 

will increase the level of effort required to obtain a WQS variance and/or make variances much more 

difficult to obtain.” Depending on the how a state or authorized tribe has been currently operating in 

regards to adopting WQS variances, EPA estimates some increased burden associated with the new 

provisions. For information on EPA’s estimates of burden see EPA’s economic analysis (EA) for the final 

rule in the docket. EPA concluded, however, that this increase in burden is reasonably balanced with the 

additional accountability, flexibility, and transparency in the WQS variance framework for the final rule 

and will allow WQS variances to be an important tool for driving water quality progress. See also 

response essay 8.a and 8b regarding general concerns related to WQS variances and response essay 12.c 

for a discussion on EPA’s estimates of burden and costs of the final rule.

Commenters said: “An option should be available for States to develop a variance rule and to adopt it 

into their State rule with EPA approval. If the variance rule has been approved by EPA, each specific 

variance should not then require EPA approval as long as the variance rule is followed.” See response 

essay 8.f.i. 

Commenters said they: “recommend language ensuring that either the state or the discharger(s) 

concerned must properly fund and promptly undertake the necessary studies and complete them as 

quickly as possible.” See response essay 8.e and also response essay 8.g.v. 

Commenters said: “nothing gives EPA new authority to mandate that an EPA-approved standard, i.e., 

designated use and criteria that must apply to a water body or a portion of a water body - as specified in 

the regulatory definition of “water quality standard” – can be used for some purposes of the Act, but 

not others.” See response essays 8.f.i and 8.f.ii.

Commenters said: “EPA should require states to provide an opportunity for public review and 

demonstrate a clear showing of need prior to renewing a variance.” See response essay 8.i.

Commenters said that EPA should ensure that states be allowed to utilize a streamlined variance 

procedure, as long as the process meets all the requirements outlined in the regulations. See response 

essays 8.a, 8.f.i and section II.E of the preamble to the final rule.

Commenters question if WQS variances are consistent with the CWA and how they can help improve 

water quality. See response essay 8.b and also section II.E of the preamble to the final rule. 

Commenters said: “... federal regulations, if adopted, should allow States to continue rely on the 

demonstration under § 131.10(g) to justify a variance, without going through additional regulatory 

hoops.” See section II.E of the preamble of the final rule and Response Essay 8.m for discussion of EPA’s 

legal authority with regard to WQS variances. The discussion includes the rationale for why a WQS 

variance is time-limited and how the construct of the “highest attainable condition” enables water 

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bodies to serve the objective of the Act to restore and maintain the chemical, physical, and biological 

integrity of the Nation’s waters. See also the discussion in the preamble to the proposed rule (78 FR 

54531, September 4, 2013) that because the existing (1983 rule) lacked explicit provisions, stakeholders 

expressed confusion, inconsistency, and mixed interpretations about how, when, and where variances 

may be appropriately used. When looking at where WQS variances have been most successful, EPA 

recognizes the need for more specific regulations that “address questions such as when a variance can 

be granted, how a variance must be justified, what is required during the term of a variance, or for how 

long a variance can be granted.” Therefore, EPA concluded that regulations that go beyond just 

requiring a demonstration under 131.10(g) was necessary. EPA also notes, that under the final rule, the 

regulation provides different factors for justifying a WQS variance for a 101(a)(2) use (or subcategory of 

such a use) than for a non-101(a)(2) use (see response essay 8.g.iv for more discussion on WQS 

variances to non-101(a)(2) uses). In addition, for more detailed responses to this or similar comments, 

see response essay 8.c, 8.f.i, and 8.f.ii and other WQS variance response essays such as 8.a, 8.b, 8.d, 8.f,

8.g, 8.g.ii, 8.g.iii, 8.g.iv, 8.g.v, 8.g.vi, 8.h, and 8.i.

Commenters said: “Variances should include some type of schedule for compliance including verifiable 

actions leading to water quality standards attainment and protection of uses. EPA should strengthen the 

requirements for maintaining a variance so that this tool is used as a method of achieving water quality 

standards through responsive and verifiable actions.” See comment essay 8.b, 8.d, 8.e, 8.f.i, 8.f.ii, 8.g.iii, 

8.g.iv, and 8.h.

Commenters said: “Section F.2.a.i. states that “A waterbody variance provides time for the state or tribe 

to work with both point and nonpoint sources to determine and implement adaptive management 

approaches on a waterbody/watershed scale to achieve pollutant reductions and strive toward attaining 

the water body’s designated use and associated criteria. This requires clarification for Wisconsin, as we 

both encourage adaptive management plans for phosphorus, and allow facility-specific variances for 

phosphorus. Does EPA intend to imply that all adaptive management plans for phosphorus in Wisconsin 

must be approved by EPA? How might adaptive management apply to standard (in WI) variance 

pollutants such as chloride, mercury, and copper?” The final rule does not regulate state or tribal 

adaptive management plans. However, a WQS variance is a change to WQS and must be reviewed and 

approved or disapproved by EPA. To the extent that a state or authorized tribe includes an adaptive 

management plan in a WQS variance, EPA will review the adaptive management plan as part of the WQS 

variance submission and approve or disapprove the WQS variance. EPA cannot speculate on the specific 

requirements a state or authorized tribe may need to include in a WQS variance in order to attain the 

HAC without site-specific information. EPA recommends the commenters refer to EPA guidance and/or 

consult with their regional EPA office.

Commenters said: “Please clarify the use of the word remove in Section F.2.b.ii “The EPA’s current 

position is that before removing a designated use states and tribes must first evaluate the impact that 

point and nonpoint source controls might have on water quality.” Perhaps this should be amended to 

say “The EPA’s current position is that before removing or modifying a designated use or applying a 

variance-modified use...” “EPA agrees that the text as written was not clear. EPA agrees that WQS 

variances do not “remove” the underlying designated use or associated criteria. See response essay 8.f.ii 

and section II.E of the preamble to the final rule for additional discussion on how the underlying WQS 

stays in place for many CWA purposes (e.g., total maximum daily loads [TMDLs], CWA section 303(d)). 

EPA notes that, especially in the context of designated uses, the phrase “remove a designated use” does 

also include “modifying” or “refining” a designated use.

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Commenters said: “Inland supports the inclusion of more specific guidance and standards as to when 

variances are available to individual and multiple discharges and on a watershed basis. We urge the EPA 

to consider the variance rule in light of the policy direction of Region 10 on human water quality criteria. 

The rule should allow enough flexibility to address the long-term needs for compliance tools with very 

stringent criteria.” The final rule is intended to allow states and authorized tribes to adopt WQS 

variances to address long-term water quality challenges. See response essay 8.b, 8.c, 8.d, 8.f.i, 8.f.ii, 

8.g.ii, 8.g.iii, 8.g.iv, 8.g.v, 8.g.vi, 8.i.

Commenters said: “EPA should clarify in the preamble the relationship of Endangered Species Act (ESA) 

requirements to its approval of state adoption of state variance procedures and subsequent individual 

state-issued variances.” EPA disagrees with these commenters. EPA believes that discussion of the 

relationship between the ESA and WQS variances is more appropriately addressed in guidance rather 

than the final rule and would typically be based on case-specific information (such as whether there are 

actually endangered or threatened species present in the water body or waterbody segment subject to 

the WQS variance). EPA will consider whether this is an area where national guidance is needed. The 

commenter should contact their regional EPA office for assistance on any specific WQS variance.

Commenters said: “EPA should clarify how “adaptive management approaches” are defined.” See 

response essay 8.c.

Commenters said: “At issue in Washington State is the prospective wide use of variances by individual 

and multiple dischargers as well as those that will apply statewide for so-called problem chemicals like 

mercury and PCBs. Without strict guidelines on variances, including mandating development and 

implementation of pollution minimization plans, as well as highest achievable water quality limits, they 

are likely to serve solely as unfettered licenses to pollute. With the prospective near-term promulgation 

of new human health criteria in Washington State, compliance tools like variances are a key element the 

state is offering to give dischargers “flexibility” and “certainty”. Yet, little substance has been offered to 

provide clarity, effective implementation and assurances that such tools meet the requirements of the 

CWA and lead to improvements in water quality.” See section II.E of the preamble to the final rule for a 

discussion on how the final rule increases accountability and transparency and will help to ensure 

effective implementation, including the provision at § 131.14(b)(2)(ii) that requires “documentation 

demonstrating that the term of the WQS variance is only as long as necessary to achieve the highest 

attainable condition. Such documentation must justify the term of the WQS variance by describing the 

pollutant control activities to achieve the highest attainable condition, including those activities 

identified through a Pollutant Minimization Program, which serve as milestones for the WQS variance.” 

And the provision at section 131.14(c) that requires: “Any limitations and requirements necessary to 

implement the WQS variance shall be included as enforceable conditions of the NPDES permit for the 

permittee(s) subject to the WQS variance.” See also response essay 8.b and other WQS variance 

response essays regarding the submission requirements such as 8.g.i. 8.g.ii, 8.g.iii, 8.g.iv, and 8.g.v. 

Commenters said: “EPA’s reference to using “adaptive management,” id. at 54531, in the context of 

variances is really inappropriate. There is nothing in the proposed rule that suggests that EPA is correct 

about its idea that variances will lead to attainment and if adaptive management is a serious 

consideration in this context, it will have to be included in the rule. Saying the phrase “adaptive 

management” in the preamble does not ensure that sufficient monitoring and evaluation will take place 

to even form the basis of next steps in an adaptive management scheme. And adaptive management 

requires triggers to make sure parties take those next steps. Without a reason, agencies do not engage 

in adaptive management. Without a clear process with information and deadlines they do not 

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implement it.” See response essay 8.c. as well as discussion above in this essay regarding the additional 

accountability and transparency in EPA’s final rule to help ensure effective implementation of WQS 

variances. 

Commenters said: “The issue of EPA’s broad assertions comes up again a few paragraphs later, when 

EPA says ‘when properly applied, a variance can lead to improved water quality over time, and in some 

cases full attainment [.]’” Id. What does EPA mean by “when properly applied”? If EPA has some ideas of 

what constitutes proper application, it must include them in the rule but at a minimum it should not 

keep the states and public guessing. What is the “proper application” EPA has in mind? All EPA hints at is 

that there might be advances in treatment technologies, control practices, or changes in circumstances 

none of which appear to be related to “proper application.” EPA disagrees with these commenters. The 

final rule at section 131.14(a) specifies where, when, and for how long a WQS variance can be applied.

See discussions earlier in this essay as well as response essay 8.f., 8.h, and those response essays 

regarding the submission requirements such as 8.g.i. 8.g.ii, 8.g.iii, 8.g.iv, and 8.g.v.

Commenters said: “How specifically will a variance take advantage of any advances in treatment 

technologies that occur? There is nothing in the rule that requires on-going evaluation of what 

technologies might be developed over a 10-year period. More likely a variance will lock in a lower level 

of treatment because it has changed the goal to accept more pollution. If EPA wants something better, it 

must build it in to the definition of a variance.” EPA disagrees with these commenters. The final rule 

requires the term of any WQS variance to be no longer than necessary to achieve the HAC. The final rule 

further requires states and authorized tribes to reevaluate WQS variances with a term longer than five 

years no less frequently than every five years. To ensure that a WQS variance reflects the HAC

throughout the WQS variance term, states and authorized tribes must also adopt a provision specifying 

that the applicable requirements in the WQS variance shall be either the HAC initially adopted, or a 

higher attainable condition later identified during any reevaluation. This provision must be selfimplementing so that if any reevaluation yields a more stringent attainable condition, that condition 

becomes the applicable WQS without additional action. Where a “higher” attainable condition has been 

identified during a reevaluation, the permitting authority, upon permit reissuance, will base the WQBEL 

on this more stringent applicable WQS consistent with the NPDES permit regulation at 

section 122.44(d)(vii)(A). The final rule also requires states and authorized tribes to obtain public input 

on the reevaluations and submit the results of the reevaluations to EPA. These provisions in the final 

rule ensures that states and authorized tribes continually evaluate conditions justifying a WQS variance 

and that the WQS variance represents the HAC throughout the WQS variance term. See also response 

comment 8.c, 8.d, 8.e, 8.f.i, 8.f.ii, 8.g.iii, and 8.i.

Commenters said: “... the phrase “control practices” is exceedingly vague. It’s unclear whether it 

pertains to point, nonpoint, or both types of sources. Control practices for nonpoint sources are not 

rocket science, waiting to be developed as can be the case with point source treatment technologies. 

More often than not, nonpoint source control practices are known now but not yet required, practices 

that could be phased in or practices that being started at the outset could pay off over a 10-year time 

frame (or less).” EPA revised the preamble of the final rule to provide greater clarity when referring to 

pollutant controls. When describing “pollutant controls” in the definition of a pollutant minimization 

program (PMP) (as defined in the final rule at 131.3(p)) the preamble to the final rules states: “Pollutant 

control technologies represent a broad set of pollutant reduction options, such as process or raw 

materials changes and pollution prevention technologies, practices that reduce pollutants prior to 

entering the wastewater treatment system, or best management practices for restoration and 

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mitigation of the water body.” See also 8.g.v for a discussion of PMPs and nonpoint source (NPS) best 

management practices (BMPs). 

Commenters said: “Finally, what changes in circumstances is EPA discussing? In thinking about how a 

“circumstance” can improve water quality one tends to think of significant restoration activities, 

significant nonpoint source controls, or the closure of a point source (presumably the variance protects 

the facility from having to add significant control technologies). These are interesting scenarios and EPA 

does not suggest what a state should be required to do if in the middle of a 10-year variance there are 

such circumstances that would warrant the removal of the variance because, essentially, its assumptions

were proven to be incorrect.” EPA considers it unreasonable to expect EPA to describe the universe of 

potential circumstances that could change in situations where WQS variances are utilized. Based on 

these and other comments, EPA revised the regulation so that the final rule extensively addresses the 

potential for changing circumstances during the term of a WQS variance (see discussion above regarding 

reevaluation requirements in the final rule).

Commenters said: “Likewise, EPA does not discuss the best outcome of a variance which is that it is not 

renewed but instead point sources previously covered by a variance are able to switch to a compliance 

schedule to meet the underlying water quality standards. We understand that in Idaho this has or is 

about to occur for three municipalities that have been covered by a variance. This is the strongest 

indication that the objectives of the CWA will in fact be met rather than dodged for many years to 

come.” EPA agrees that attaining the underlying WQS (or commitment to attain the underlying WQS 

through use of a compliance schedule [CS]) is a good outcome of a WQS variance. The preamble to the 

final rule extensively discusses the relationship between WQS variances and permit CS. See also 

response essay 8.e.

Commenters said: “EPA goes on in this theme at some length, invoking the goal that variances “are 

intended to allow incremental environmental progress in achieving designated uses,” “variances will 

allow for environmental progress towards achieving the goals of the CWA,” and “[the proposed] 

revisions will also provide assurance that further feasible progress towards the designated use and 

criterion will be made during the variance period.” Id. at 54532. Yet there is very little in the proposed 

rules that would result in this outcome other than, perhaps, the proposed 40 C.F.R. § 131.14(d) 

regarding renewals of variances. This, of course, would only come after a 10-year period, or some 

increment of 10 years. As between, for example, (1) a state ensuring that significant nonpoint source 

controls are implemented in the first 10 years of a variance and (2) an NPDES source betting it could 

count on EPA to approve a renewed variance in the absence of any nonpoint source controls instead of 

vetoing a permit and denying a variance renewal, thereby requiring expensive treatment technology, we 

would bet on the latter and win every time. That’s why the rules need to be very clear about the 

expectations and why it is not sufficient to simply repeat numerous times what the goal is, and what 

EPA hopes will happen. Very little that involves spending money to achieve pollution reductions takes 

place on the basis of hope.” EPA has developed a final rule that provides states and the Agency with 

appropriate requirements to achieve the goals of WQS variances as articulated in the preamble. See 

section II.E of the preamble to the final rule and response essays 8.b and 8.g.v.

Commenters said: “We also caution EPA against using the phrase “legacy pollutants” as it does in the 

discussion of when variances might be useful. Id. at 54532 (“challenges involving legacy pollutants”). 

While we agree that a variance is preferable to a permanent downgrade in designated uses where a 

state and the public do not know whether a use can be attained, the word “legacy” is meaningless. It is 

often used to mean now-banned toxic pollutants but in reality it can be extended to mean nearly any 

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impaired waterbody including those with impairments that have developed since 1975. It’s certainly 

true of the Oregon Department of Agriculture which considers nearly any riparian impairment to be 

“legacy.” Even people who might disagree with that outlook might view widespread overgrazing that has 

removed riparian vegetation and affected the temperature regime of streams in the West as a “legacy” 

condition. Since it is ill-defined and not susceptible to definition EPA should avoid using it and use 

examples instead.” EPA generally agrees with these commenters and avoids using the term “legacy 

pollutants” in the final rule.

Commenters said: “Full transparency requires, at a minimum, that once approved by EPA a state provide 

the information on its website. We recommend that states be required to post with their water quality 

standards some method by which the public is alerted to the fact that variances exist and that they 

change over time. If variances are merely buried in standards, they will be a lot less obvious. Moreover, 

to ensure consistency with the findings and rationale EPA used to approve a variance, states should be 

required to post EPA’s decision document for the duration of the variance. As EPA likely knows, its 

regions handle standards issues inconsistently with regard to providing information to the public; some 

regions post standards information for long periods of time, some for short periods of time, and some 

do not even recognize that water quality standards have been issued and approved by EPA in their 

states. Posting the rationale will help members of the public comment on other regulatory documents 

that are linked in some fashion to the variance or its rationale including but not limited to NPDES 

permits, 401 certifications, TMDLs, 303(d) lists, and nonpoint source plans and practices. We urge EPA to 

include this requirement in rules because we have seen states repeatedly promise EPA to post 

information on their websites with no subsequent action from states. EPA must do more than invoke 

“transparency,” it must ensure it.” As EPA discussed in the preamble to the proposed rule, CWA section 

101(e) provides that “public participation in the development, revision, and enforcement of any 

regulations, standard, effluent limitation, plan, or program established [...] under this Act shall be 

provided for, encouraged, and assisted [...].” EPA maintains a WQS repository on its website where the 

public can obtain all approved WQS. In addition, EPA’s decision documents are public information and 

can be requested through the relevant EPA regional office. EPA also encourages states and authorized 

tribes to make WQS publically available on their websites (e.g., the preamble to the final rule 

recommends states and authorized tribes provide a list of the dischargers covered under a WQS 

variance on their websites or other publicly available sources of state or authorized tribal information, 

particularly when using multiple discharger WQS variances). 

Commenters said: “As for public participation, we urge EPA to include in the preamble its view that 

states may not hide variance requests in NPDES permit commenting opportunities. In other words, 

states must specifically request public comment on variances just as they do for other water quality 

standards. While we think the rules are clear on this because they cite to 40 C.F.R. § 131.20(b), some 

states believe they can merge the public process for a permit renewal with a variance. Members of the 

public who might not comment on a permit renewal might be interested in commenting on a 10-year 

variance. This is not transparent.” EPA disagrees that combining the public process required for a WQS 

variance and NPDES permit is “not transparent.” EPA believes that states and authorized tribes may 

leverage the public process that they currently use for NPDES permit issuance for obtaining public input 

on the WQS variance when that process is consistent with EPA’s regulations at section 131.20(b), 

including holding a public hearing. The public notice must make clear that the state or authorized tribe is 

also proposing to revise the WQS by adopting a WQS variance. Once the WQS variance is adopted, they 

can submit the WQS variance to EPA for approval or disapproval under CWA section 303(c). EPA notes 

that the final rule also requires public input on the reevaluation for any WQS variance with a duration 

greater than five years. 

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Commenters suggested the following regulatory text: “[begin new text] (4) A WQS variance shall not be 

granted if the designated use and criterion remove necessary protections from existing uses. [end new 

text]. [begin new text] (5) A WQS variance shall not be granted if the designated use and criterion 

addressed by the proposed WQS variance can be achieved through implementation of cost-effective and 

reasonable best management practices for point or nonpoint source controls related to the pollutant(s) 

and location(s) in the variance and are within the authority of the permittee to control. [end new text].” 

See response essays 8.f and 8.g.v. 

Commenters said: “Added in redline edits above are: (1) protection of existing uses in the issuance of 

variances; (2) a requirement that the variance state both the effluent condition and the replacement 

criterion; (3) a five year limit on variances; (4) a plan for achieving implementation of BMPs including 

timeframes, methods of assuring implementation, and a monitoring plan; (5) a requirement that the 

permittee implement any BMPs within its authority to do so; (6) a restriction on lowering water quality 

through changes in mixing zones; and (7) a requirement that the state implement the plan to ensure 

BMPs. Removed in redline edits above are: (1) waterbody variances; (2) applicability of variances to 401 

certifications except 401 certifications related to NPDES permits; (3) 10-year variances; and (4) limitation 

on uses established in CWA section 101(a)(2).” See response essay 8.b, 8.c, 8.f, 8.f.i, 8.f.ii, 8.g.ii, 8.g.iii, 

8.g.iv, and 8.g.v.

Commenters said: “The Water Protection Groups strongly agree that variances can never be an option 

for new or expanding discharges as such a concept is completely contrary to the requirements of the 

Clean Water Act and existing EPA regulation. EPA’s proposal that a state must demonstrate that 

attaining the designated use and criteria is not “feasible” during the term of the variance is confusing. 

“Feasible” is a term that is often subject to much controversy and should be better defined. The Water 

Protection Groups submit that EPA should not allow “feasible” to be defined in strictly monetary terms, 

but should limit it to whether a technology or practice is actually available to address a water quality 

issue. If there is truly no available method, then perhaps attaining a water quality standard in three 

years is not “feasible.” (Although again, there is nothing in the Clean Water Act that allows for a variance 

in that instance-it will simply take longer for a water body to come off the impaired waters list.). Finally, 

some of the same concerns with vague loopholes expressed above in the section regarding UAAs would 

apply here and the Water Protection Groups urge EPA to tighten those requirements.” EPA disagrees 

with these commenters. See response essays 8.g.iv, 8.f.i, and 8.f.ii. Also, in regards to the term 

“feasible,” EPA has used the term in its regulations at section 131.10 since 1983 and has not found the 

term to be confusing and is not strictly defined in monetary terms. There are five factors in section 

131.10(g) that are not related to monetary terms. In relation to a WQS variance to CWA 101(a)(2) uses 

and subcategories of such uses, the term “feasible” has the same meaning as in part section 131.10, 

however it is limited by time. Meaning the underlying designated use is not feasible to attain within the 

time identified as the term of the WQS variance.

Commenters said: “public safety [should] be included in determining whether a water quality variance is 

appropriate for a water body as part of Section 131.14.b.3, particularly with respect to meeting water 

quality standards for chloride in relation to deicing material usage. MassDOT constantly strives to 

balance the public safety needs during winter storm conditions and minimizing the potential 

environmental impacts. Utilization of a water quality variance may likely be an appropriate regulatory 

mechanism to allow time to deploy additional technology and equipment that may be needed in pursuit 

of meeting aquatic life water quality standards for chloride in the smallest of streams with limited 

dilution. Reducing deicer material usage (if possible) requires time to achieve iterative steps and 

measured progress to allow operators and the traveling public to adjust to incremental changes while 

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maintaining safe driving conditions.” The factors in the final rule that states and authorized tribes can 

use to justify a WQS variance are adequate to address this scenario. For a WQS variance to a 101(a)(2) 

use, the final rule requires states and authorized tribes to submit a demonstration that the use and 

criterion are not feasible to attain based on one of six factors in section 131.10(g) or a new factor 

related to lake, stream, or wetland restoration. EPA cannot speculate on the outcome of a WQS variance 

submission to a hypothetical scenario without specific data and information on the particular 

circumstances. See also response essay 8.g.iv.

Commenters said: “recognizing that legitimate factors may prevent EPA or a state from acting on a 

renewal application before the expiration of the original variance term, we urge EPA to add an 

“administrative continuance” mechanism similar to the one for expiring, administratively continued 

NPDES permits under 40 CFR §122.6. As long as a renewal application is timely and complete, then the 

discharger should continue to enjoy the protections of the variance pending a state’s or EPA’s action on 

the application.” See response essays 8.g.iii.

Commenters said: “EPA should consider allowing states the authority to issue variances 

programmatically. EPA could approve a state variance development and approval process described in 

state standards and allow the state, under clear conditions, to issue a variance through rulemaking, 

without discrete EPA approval. For example, if a state were to adopt procedures and requirements for 

issuing waterbody-specific or multi-discharger variances in their water quality standards and obtained 

EPA approval, then subsequent individual variances could be issued by the state under the framework of 

the approved water quality standards without having to obtain individual EPA approval. The state could 

use its NPDES delegated authority to issue and manage the individual variances, including the public 

processes that are built into that program. This would allow administrative efficiencies for both the state 

and EPA while at the same time providing a fully transparent public process through the NPDES 

program.” See response essays 8.a, 8.c., and 8.f.i. See also section II.E of the preamble for a discussion 

on how to streamline the WQS variance process.

Commenters said: “While U.S. EPA suggests that variances can create a framework to provide States and 

tribes with time to implement adaptive management approaches, the prescriptive requirements and 

oversight of the minutiae make this process unattractive. If a State is going to undertake the task of 

performing the assessment in section 131.10(g), it might as well remove the use instead of having to 

deal with a short-term variance process that may need to be repeated one or more times. EPA should 

make the variance process much more streamlined since it is only applicable for a relatively short 

duration.” See response essays 8.a, 8.b, 8.c, 8.d, 8.f.i, and 8.f.ii.

D. General Support

EPA appreciates the time and effort to provide comments. 

E. Clarification about Need for State or Tribal Variance Authorizing Provision

Commenters suggested that EPA include in the final rule: “clarification regarding state authorization for 

variances. Specifically, will states need to add authorizing language for variances into their state water 

quality standards?” As described in section II.E of the preamble to the final rule, because EPA must 

review and approve a WQS variance as consistent with the final rule at section 131.14, “states and 

authorized tribes are not required to adopt specific authorizing provisions into state or authorized tribal 

law before using WQS variances consistent with the federal regulation.” However, the regulation does 

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not prohibit states or authorized tribes from adopting authorizing provisions as long as they are 

consistent with the federal regulations.

F. Specific Provisions That Should Be Included in the Final Rule

Commenters said: “If EPA proceeds with formalizing a variance rule, it should amend the Proposed Rule 

to make it consistent with its long-standing practice for issuing variances by including the following: • 

Each individual variance is included as part of the water quality standard; • The justification submitted 

by the State includes documentation that treatment more advanced than that required by sections 

303(c)(2)(A) and (B) has been carefully considered, and that alternative effluent control strategies have 

been evaluated; • The more stringent State criterion is maintained and is binding upon all other 

dischargers on the stream or stream segment; • The discharger who is given a variance for one 

particular constituent is required to meet the applicable criteria for other constituents; • The discharger 

either must meet the standard upon the expiration of this time period or must make a new 

demonstration of “unattainability”; • Reasonable progress is being made toward meeting the standards; 

and • The variance was subjected to public notice, opportunity for comment, and public hearing. (See 

section 303(c)(l) and 40 CFR 131.20.) The public notice should contain a clear description of the impact 

of the variance upon achieving water quality standards in the affected stream segment.” 

EPA agrees with the commenters that each individual variance must be a WQS. The final rule requires 

states and authorized tribes to adopt any WQS variance into state or tribal WQS and submit them to 

EPA for approval or disapproval. It has been EPA’s practice to have an analysis of alternative effluent 

control strategies as part of a variance demonstration, and EPA expects this will continue to be the 

practice to meet the requirements of the final rule as states and authorized tribes justify the need for 

the WQS variance, identify the HAC, and justify the duration of the WQS variance. EPA agrees with the 

commenters that “the more stringent State criterion is maintained and is binding upon all other 

dischargers on the stream or stream segment.” The final rule specifies: “A WQS variance may be 

adopted for a permittee(s) or water body/waterbody segment(s), but only applies to the permittee(s) or 

water body/waterbody segment(s) specified in the WQS variance.” EPA agrees with the commenters

that the “discharger who is given a variance for one particular constituent is required to meet the 

applicable criteria for other constituents.” The final rule specifies: “All other applicable standards not 

specifically addressed by the WQS variance remain applicable.” EPA agrees with the commenters that 

the “discharger either must meet the standard upon the expiration of this time period or must make a 

new demonstration of ‘unattainability.’” The final rule specifies that a subsequent WQS variance must 

be consistent with section 131.14. EPA agrees with the commenters that an approval or disapproval 

decision for a subsequent WQS variance should consider the progress made toward the underlying 

designated use. EPA believes the requirement to represent the HAC, together with five-year reevaluations, effectively pursue “reasonable progress” in a more structured manner. EPA agrees with the 

commenters that all WQS variances must be subjected to public notice and comment. The final rule 

requires all WQS variances to be subject to public participation requirements at section 131.20(b). 

Commenters said: “If EPA insists on including variances in its proposed revisions, it should modify the 

language in accordance with the following suggestions: 1. Only allow variances on waters where a TMDL 

has been approved and identifies interim actions with enforceable milestones as part of the variance. 

EPA disagrees with these commenters. While WQS variances affect the development of WQBELs for the 

discharger(s) specified in the variance and are intended to support restoration, they do not affect the 

underlying designated use and criterion that apply to the rest of the water body. That is, variances do 

not change the long term goals for the waterbody. TMDLs, on the other hand, are developed to achieve 

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the long term goals of the waterbody and are thus based on the underlying designated use. Because the 

purposes of these two tools are different, milestones for progress in a variance are not a replacement 

for establishing a TMDL for impaired waters. However, where variances are approved for multiple 

dischargers on the same impaired water (or there is an approved waterbody variance) and development 

of a TMDL is projected, the state/tribe has some flexibility to consider the relative priority of that 

particular TMDL while incremental progress is made through the variance(s).” See also response essay 

8.f.ii.

Commenters also said: “2. Do not allow variances to delay implementation of all known and achievable 

methods of toxic pollution elimination from point source discharges.” Although the intended meaning of

“achievable” and “delay,” is not clear, if “achievable” means “attainable”, and “delay” does not include a 

schedule of compliance (where authorized), then the final rule does not delay implementation of 

achievable methods of toxic pollution elimination from point source discharges. The final rule requires 

states and authorized tribes to submit documentation demonstrating that the underlying designated 

use is not attainable, to specify the requirements of the WQS variance as the HAC, and to specify a WQS 

variance term that is only as long as necessary to achieve the HAC. 

Commenters said: “3. Do not allow variances to cause delays in establishment of final water qualitybased effluent limits (“WQBELs”) in NPDES permits for protection of all beneficial uses.” The commenter

does not fully explain what is meant by: “cause delays in establishment of final water quality-based 

effluent limits (“WQBELs”) in NPDES permits for the protection of all beneficial uses”. If the beneficial 

use is not attainable, then establishing an associated WQBEL will not by itself protect the beneficial use.

If the commenter means that a state or authorized tribe should not be able to use a WQS variance to 

delay making progress that is attainable, the final rule requires the term of a WQS variance to be only as 

long as necessary to achieve the HAC. 

Commenters said: “4. Expressly state that dischargers will be required to implement pollutant control 

strategies and end-of-pipe treatment well beyond “technology-based” considerations including, but not 

limited to, raw-product replacement, source reduction through protective municipal pretreatment 

programs, specific storm water toxics reduction strategy, and complete elimination of the toxic 

discharge using zero-discharge technologies (i.e., flow reduction and water reclamation).” EPA agrees 

with the general intent of these comments, but disagrees with the suggested text. The final rule requires 

WQS variances to express the HAC. For example, for discharger-specific WQS variances the HAC must be 

expressed as a quantifiable expression of: the highest attainable interim criterion, an interim effluent 

condition that reflects the greatest pollutant reduction achievable, or if no additional feasible pollutant 

control technology can be identified, the interim criterion or interim effluent condition that reflects the 

greatest pollutant reduction achievable with the pollutant control technologies installed at the time the 

State adopts the WQS variance, and the adoption and implementation of a PMP. As discussed previously 

in this essay, “pollutant control technologies (within the definition of PMP) represent a broad set of 

pollutant reduction options, such as process or raw materials changes and pollution prevention 

technologies, practices that reduce pollutants prior to entering the wastewater treatment system, or 

best management practices for restoration and mitigation of the water body.” See also 8.g.v for a 

discussion of PMPs and NPS BMPs. The final rule further specifies that the WQS variance serves as the 

applicable WQS for implementing NPDES permitting requirements pursuant to section 122.44(d), and 

that any limitations and requirements (emphasis added) necessary to implement the WQS variance shall 

be included as enforceable conditions of the NPDES permit.

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Commenters said: “Approval of a variance should also not preclude states from subsequently initiating 

(and completing) procedures to remove or modify the affected use(s) with supporting UAA, if such an 

action is deemed to be appropriate at some point in the future. The variance process considers 

uncertainties such as development of future treatment technology required to attain the full designated 

use the variance applies to. After further evaluation, it may become apparent that full use attainment is 

infeasible at which point the receiving water may need to be reclassified on a more permanent basis.” 

EPA agrees with these commenters. The final rule does not preclude states from subsequently initiating 

(and completing) procedures to remove or modify the affected use(s) with supporting use attainability 

analyses (UAA), if such an action is deemed to be appropriate at some point in the future.

Commenters said: “We recommend that EPA modify 131.14(b)(2) as follows to ensure that any variance 

will ultimately lead to attainment of designated uses: First, the State/Tribe should analyze how the 

“highest attainable condition” during the term of a variance (131.14(b)(1)(ii)(B)) would relate to actual 

attainment of the designated use. Since the purpose of a WQS variance is “incremental environmental 

progress” towards such ultimate attainment (see proposed rule, p. 58), this analysis would help the 

State/Tribe and EPA to determine what additional progress would be necessary to achieve attainment 

once the variance expires. Second, the State/Tribe should include alternatives in its analysis, in order to 

demonstrate that the proposed WQS variance requires the most expeditious feasible progress towards 

attainment.” 

EPA partially agrees with these commenters. EPA agrees that it is important to be able to track progress 

toward the underlying designated use when utilizing a WQS variance, especially when the term of the 

WQS variance is long. However, EPA disagrees with the commenters that the regulation should require 

states and authorized tribes to analyze how the HAC relates to actual attainment of the designated use

for all WQS variances. The final rule requires states and authorized tribes to submit to EPA 

documentation demonstrating the need for the WQS variance. EPA expects such documentation to

include the analyses that were used to determine that the underlying designate use is not attainable, 

the analyses that were used to determine the highest attainable use (HAU) and to justify the duration of 

the WQS variance. As stated in section II. E of the preamble to the final rule and in previous subsections 

of this essay, for WQS variances longer than five years, the final rule requires states and authorized 

tribes to reevaluate WQS variances at least every five years and includes a set of additional related 

provisions to ensure the reevaluations occur on the set schedule, include public input, and that the 

results can be used by permitting authorities for reissuance of permits without additional EPA approval 

of any higher attainable condition found during a reevaluation. EPA believes that establishing these 

reevaluation requirements for WQS variances longer than five years is the best way to achieve EPA’s 

policy objective of active, thorough, and transparent reevaluation by states and authorized tribes while

minimizing rulemaking burden. The reevaluation requirements in the final rule eliminate the need to 

specify a maximum WQS variance term because they ensure the HAC is always the applicable WQS 

throughout the WQS variance term, thus driving incremental improvements toward the underlying

WQS. EPA chose five years as the maximum interval between reevaluations because five years is the 

length of a single NPDES permit cycle, allowing the reevaluation to inform the permit reissuance 

process. 

As discussed in the preamble to the final rule, WQS variances remain subject to the triennial review and 

public participation requirements specified in section 131.20. This requirement ensures that the public 

has the opportunity to work with states and authorized tribes in a predictable and timely manner to 

search for new or updated data and information specific to the WQS variance that could indicate a more 

stringent HAC exists than the state or authorized tribe originally adopted. “New or updated data and 

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information” includes, but is not limited to, new information on pollutant control technologies, changes 

in pollutant sources, flow or water levels, economic conditions, and BMPs that impact the HAC. Where 

there is an EPA-approved WQS variance, the permitting authority must refer to the reevaluation results 

when reissuing NPDES permits to ensure the permit implements any more stringent applicable WQS 

that the reevaluation provides.

EPA generally agrees that the states and authorized tribes “should include alternatives in its analysis, in 

order to demonstrate that the proposed WQS variance requires the most expeditious feasible progress 

towards attainment.” However, EPA disagrees that it is necessary to include such an explicit 

requirement in the final rule as an analysis of alternatives is inherent in the analyses needed to 

demonstrate the need for a WQS variance, including the analyses that were used to determine that the 

underlying designated use is not attainable, and the analyses that were used to determine the HAU, and 

the justification of the duration of the WQS. The documentation the state or authorized tribe submits 

with the WQS variance for review and approval or disapproval will inform EPA’s review and evaluation 

of whether the state’s or authorized tribe’s submission sufficiently justifies the need and the term of 

WQS variances.

Commenters said: “Additionally, variances are required to be set at the highest attainable condition as 

opposed to the highest attainable use - a term of art previously defined in the proposed regulations. We 

commend EPA for encouraging temporary standards that are as protective as possible, but fear that that 

“highest attainable condition” currently lacks clarity, because it introduces a new undefined term and 

raises questions how this should be defined vis-à-vis the newly proposed definition of highest attainable 

use. Moreover, what is “attainable” is highly subjective, and authorizes applicants to determine the fate 

of WQS and ultimately the level of resource protection. Given that a variance effectively re-writes a 

state WQS for a specific place or permit, EPA needs to clarify how those standards will be developed, 

and how they will protect uses and meet the goals of the Act. At a minimum, in order to provide clear 

direction to states, variance justifications, should have to follow same process as UAA, and scientific and 

economic analysis must be equally rigorous.” See response essays 8.c and 8.g.ii. See also section II.E of 

the preamble to the final rule for a discussion comparing the “rigor” for a WQS variance and a use 

change.

Commenters said: “Another significant problem with the proposed language is the lack of provisions 

which will provide assurances that variances or compliance schedules will result in eventual attainment 

of WQS. For example, proposed rules for variances require that reasonable BMPS that “could be 

implemented,” get documented. This provision merely requires the documentation of a scant 

possibility, and requires no reasonable assurances that implementation will occur. Moreover, EPA 

provides that the variances can be renewed, largely indefinitely, even in the face of continued variance 

noncompliance. These provisions fail to provide the necessary assurances of CWA compliance and the 

protection of treaty reserved resources.” See response essays 8.d, 8.e, 8.i, and 8.g.v. 

Commenters said: “EPA should explicate how these processes, if used at all, will provide clear-cut 

assurances that WQS can be attained in a timely manner. This should include clear direction that 

nonpoint source controls are not only identified, but are in fact are clearly prescribed to be consistent 

with achieving WQS, and implemented in a timely manner to ensure that standards are attained as fast 

as possible. It should also prevent lengthy excursions from state standards when non-compliance 

remains the modus operandi. Absent such assurances, variances and compliance schedules will be 

nothing more than exemptions from the CWA.” See response essay 8.g.v.

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G. Effective Date of the Final Rule

Commenters said that EPA’s proposed requirement that variances issued by states comply with the 

federal rule immediately following the final rule adoption date is unreasonable, and that EPA should 

include either a delayed effective date or “a future date for state rules to comply.” EPA took the 

commenters concerns into account and revised the effective date section of the preamble. The 

preamble of the rule explains that although states and authorized tribes are subject to the requirements 

of the final rule on the effective date of the rule, EPA’s expectation is that, where a new or revised 

requirement necessitates a change to state or authorized tribal WQS, such revisions will occur within the 

next triennial review that the state or authorized tribe initiates after publication of the rule. In addition, 

the section explains how EPA intends to review WQS that are in the adoption process when the rule 

becomes effective. With these changes, EPA believes it has addressed the concerns of the commenters 

in a manner that is consistent with the effective dates for new rules. The commenters should refer to: 

“I.E. When Does this Action Take Effect” in the preamble to the final rule for more information and 

section II.E for a discussion that is specific to previously approved WQS variances and variance 

procedures or policies. 

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Essay 8.m – Variances: EPA’s Legal Authority

A. General

A number of commenters expressed concerns that section 131.14 would interfere with the states’ role

in adopting and implementing water quality standards (WQS). For instance, one commenter stated that 

the U.S. Environmental Protection Agency (EPA) failed to “identify any justification for interfering with 

the states’ authority to make assessments based on local conditions in the manner proposed.” In a 

similar vein, another comment expressed the position that “variance adoption and implementation 

should be left to the states since they are in a better position to address specific concerns and needs.” 

Another commenter asserted that the requirements of section 131.14 “improperly extend EPA’s 

approval authority over matters in which states should continue to be afforded greater deference and 

flexibility.” The commenter acknowledged that section 131.14 “would achieve national uniformity for 

WQS variance implementation” but believed that EPA’s approval authority should be limited to state 

variance policies and not individual WQS variances.

EPA recognizes that states and authorized tribes and their public are in the better position to evaluate 

local concerns and needs. The final rule does not interfere with that relationship or the authority of 

states or authorized tribes to make these assessments. Rather, the final rule specifies baseline 

requirements that any WQS variance would need to be consistent with if a state or authorized tribe 

decides to adopt a WQS variance. The requirements will ensure the consistent application of WQS 

variances for the states and authorized tribes. As discussed elsewhere, the states issuing the greatest 

number of variances are states subject to the variance regulation applicable to the Great Lakes. (Title 40

of the Code of Federal Regulations (CFR) Part 132, Appx F, Proc.2). Those detailed regulations have 

fostered, not interfered with, those states’ adoption of variances. Those are variances that comply with 

consistent baseline requirements and allow temporary modifications to WQS allowing progress to be 

made toward attainment of WQS rather than permanently downgrading of WQS. See also EPA’s 

response essay 3.a concerning state primacy in the WQS program.

As discussed in the preamble to the proposal (78 Fed. Reg. 54531 -532), the final rule is consistent with 

and authorized by the Clean Water Act (CWA). In regard to treating all WQS variances as WQS subject to 

review and approval, the requirements in the final rule also are consistent with EPA’s guidance and 

implementation of WQS variances since the 1970’s. Because individual WQS variances have always been 

considered to be modifications to WQS, the final rule requires states to and authorized tribes to adopt 

WQS variances as new or revised WQS and submit them to EPA for review and approval. This includes a 

decision to adopt a subsequent WQS variance. Some commenters said EPA’s review and approval of a 

variance “renewal” was not previously required and EPA was removing power and discretion from the 

states. Contrary to the commenter’s understanding, this is not a new position. EPA’s position has been 

that adoption or subsequent adoption (or renewal after expiration) of a WQS variance was subject to 

EPA review and approval. In response to the comment that EPA should only review state variance policy, 

EPA disagrees because individual WQS variances are new or revised WQS and as such require EPA 

review and approval. See also response Essay 8.f.i for additional discussion on EPA’s consideration of 

WQS variances, not just variance policies or procedures to be WQS. Also, see response Essay 8.i for a 

discussion on “renewal” of WQS variances. 

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Adoption of WQS variances through the WQS adoption process ensures that the public is made aware 

that a WQS change is under consideration and has sufficient opportunity to comment on the WQS 

variance. The final rule also ensures the state and tribal standards reflect the applicable standards (the 

WQS variance) that will be used to derive effluent limitations. States and authorized tribes may use their 

adoption and implementation procedures so long as they comply with the requirements in section

131.14. EPA disagrees with the comments that allege that there is “so much ambiguity and ‘guidance’ in 

the rule” that EPA “would acquire largely unbridled power to deny state submittals or require more 

information.” EPA considers the final rule to set forth very clear and well defined provisions on 

applicability, requirements for submission, and implementation of WQS variances in National Pollutant 

Discharge Elimination System (NPDES) permits. EPA carefully considered all comments on the proposed 

rule and made revisions in response to those comments to help ensure the final rule was clear, achieved 

the objectives for authorizing WQS variances and would be implementable by the states and authorized 

tribes in a consistent and transparent way.

Another commenter criticized the provisions in section 131.14 related to identifying and documenting 

best management practices (BMPs) for nonpoint source (NPS) controls. The commenter stated that 

these provisions “plainly would usurp authorities that Congress reserved to states and tribes under the 

CWA, violate longstanding EPA policy acknowledging that reservation, and interfere with exclusive state 

control (rather than mere regulatory primacy) over controls and methods related to nonpoint sources, 

as established by Congress and confirmed by federal courts.” The commenter went on to say that “it 

would be arbitrary and capricious and contrary to law for EPA to coerce states into taking particular 

courses of action that EPA itself has no regulatory authority to pursue, and which Congress expressly 

reserved to states and tribes.” EPA disagrees with the commenter. EPA’s final rule does not usurp the 

authorities of states or authorized tribes to regulate NPS of pollution nor does the final rule coerce 

states or authorized tribes. The final rule only requires information regarding BMPs for NPS controls be 

provided and considered during the process of evaluating whether to adopt a WQS variances applicable 

to a water body or waterbody segment. It is reasonable and appropriate in adopting such a WQS 

variance to consider the role of NPS in causing or contributing to the nonattainment of WQS. Similarly it 

is reasonable and appropriate in considering whether to adopt a subsequent WQS variance applicable to 

a water body or waterbody segment whether BMPs for NPS that are causing or contributing to the 

nonattainment are being implemented and whether they are effective. The purpose of a WQS variance 

is to make feasible progress toward attaining WQS and information on BMPs for NPS controls is 

important in deciding whether this type of variance is appropriate. For further discussion on BMPs for 

NPS see response Essay 8.g.v.

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