OFFICE OF INSPECTOR GENERAL

Catalyst for Improving the Environment 

Evaluation Report 

Efforts to Manage Backlog of 

Water Discharge Permits 

Need to Be Accompanied by 

Greater Program Integration 

Report No. 2005-P-00018 

June 13, 2005 
Report Contributors: 

Abbreviations 

Ira Brass 

Susan Barvenik 

Thomas Herrod 

Carolyn Bowers 

Dave Cofer 

James Haller 

ASIWPCA Association of State and Interstate Water Pollution Control Administrators 

CAFO Concentrated Animal Feeding Operation 

EPA Environmental Protection Agency 

ePIFT Electronic Permit Issuance Forecasting Tool 

FMFIA Federal Managers’ Financial Integrity Act 

FY Fiscal Year 

GPRA Government Performance and Results Act 

ICIS Integrated Compliance Information System 

NPDES National Pollutant Discharge Elimination System 

OIG Office of Inspector General 

OWM Office of Wastewater Management 

PCS Permit Compliance System 

PER Permitting for Environmental Results 

TMDL Total Maximum Daily Load 

WLA Waste Load Allocation 
U.S. Environmental Protection Agency 2005-P-00018

Office of Inspector General June 13, 2005

At a Glance 

Catalyst for Improving the Environment 

Why We Did This Review 

The Environmental Protection 

Agency (EPA) has been

concerned about the backlog

of expired National Pollutant

Discharge Elimination System

(NPDES) permits for a

number of years. We sought

to determine: 

• how successful EPA and 

States have been in 

eliminating the backlog; 

• the potential environmental

impact of the backlog; and 

• how well measures reflect 

environmental impacts. 

Background 

The NPDES permit program,

established by Congress,

regulates discharges from

point sources to water bodies.

The goal is to reduce the

discharge of pollutants to

protect and improve water

quality. Permits need to be 

renewed every 5 years. As of 

June 2003, EPA reported that

the backlog of expired permits

needing renewal consisted of

1,120 major permit facilities,

as well as 9,386 individual 

minor and 6,512 general

minor permit facilities. 

For further information, 

contact our Office of 

Congressional and Public 

Liaison at (202) 566-2391. 

To view the full report, 

click on the following link: 

www.epa.gov/oig/reports/2005/ 

20050613-2005-P-00018.pdf 

Efforts to Manage Backlog of Water Discharge Permits 

Need to Be Accompanied by Greater Program Integration

 What We Found 

EPA and the States have had varying success in eliminating the backlog of

NPDES permits requiring renewal, and more still needs to be done. The NPDES 

permit program is only one of many EPA programs to improve surface water

quality. EPA needs to integrate its efforts to eliminate the NPDES backlog with

the other programs to improve and maintain water quality based on Clean Water

Act requirements. 

To eliminate the NPDES permits backlog, EPA needs to address challenges

involving resource constraints, increasing workload, complex permitting issues,

external sources of permitting delays, and oversight limitations. EPA is now 

managing the NPDES permit program through the “Permitting for Environmental

Results” Strategy that increases focus on environmental outcomes. 

Only a small portion of waters currently identified as being “impaired” are

associated with backlogged permits. While the majority of backlogged permits

renewed had changes to discharge limits, the majority of the controls in the prior

permits generally did not appear to change. A large number of the new permits 

contained limits for new parameters. Prioritizing permitting resources according

to potential environmental impact could result in greater environmental benefits. 

The significance of the backlog could grow as a result of increased efforts in other

water protection programs that may necessitate NPDES permit revisions. 

EPA’s reporting on the NPDES backlog measure under the Government

Performance and Results Act did not provide an accurate view of the program

status or an adequate measure of environmental results. Prior to Fiscal Year 2005 

revisions, the measures did not properly compare progress against baselines, and

the measures focused on outputs (tasks performed) rather than outcomes

(environmental results achieved). EPA had recognized these weaknesses and

begun taking corrective actions.

 What We Recommend 

EPA needs to build on the steps already initiated to reduce the NPDES permit

backlog. We made various recommendations to EPA to assist the Agency in such 

efforts. EPA needs to take various steps to integrate the NPDES permit program

with other point source programs that support the permit program. This would 

include creating a system for assessing the effectiveness and efficiency of its

efforts related to clean water. EPA also needs to continue making improvements

related to its measures, such as providing appropriate baselines. EPA provided

extensive comments in response to our draft report. The Agency emphasized that

through the “Permitting for Environmental Results” Strategy it is taking steps to

reduce the NPDES backlog and in general improve the quality of the Nation’s

water bodies. We encourage EPA to continue refining this strategy. 
UNITED STATES ENVIRONMENTAL PROTECTION AGENCY 

WASHINGTON, D.C. 20460 

OFFICE OF 

INSPECTOR GENERAL

June 13, 2005 

MEMORANDUM 

SUBJECT: Efforts to Manage Backlog of Water Discharge Permits 

Need to Be Accompanied by Greater Program Integration 

Report No. 2005-P-00018 

FROM: Dan Engelberg /s/ 

Director, Water Issues – Office of Program Evaluation 

TO: Benjamin Grumbles 

Assistant Administrator, Office of Water 

This is the final report on the subject evaluation conducted by the Office of Inspector General 

(OIG) of the U.S. Environmental Protection Agency (EPA). The cooperation of all EPA regions 

and 15 States contributed significantly to this report, and their participation is appreciated. 

This report contains findings that describe the issues identified by the OIG and recommended 

corrective actions. This report represents the opinion of the OIG, and the findings do not 

necessarily represent the final EPA position. Final determinations on matters discussed in this 

report will be made by EPA managers in accordance with established audit resolution 

procedures. 

On January 25, 2005, the OIG issued a draft report to EPA for review and comment. A response 

was submitted on March 15, 2005, and an exit conference held on March 31, 2005. EPA's 

response emphasized the importance of the Permitting for Environmental Results (PER) Strategy 

established in 2004 for managing the NPDES program. EPA overall agreed that while the 

backlog alone may not provide an effective strategy to improve water quality, permits are a key 

element in the structure and implementation of the Clean Water Act. Further, EPA stated that 

the permit prioritization effort, under the PER Strategy, is intended to help the NPDES program 

strike the proper balance between the continuing effort to reduce the backlog and the need to 

ensure the timely issuance of the most environmentally significant permits. EPA provided 

comments, clarifications, and additional information on areas in the report and generally 

concurred, with suggested modifications, to our recommendations. EPA also provided 

information on ongoing activities in some of these areas. The OIG has incorporated these 

comments, technical corrections, and supplemental information into the final report. 
Action Required 

In accordance with EPA Manual 2750, you are required to provide a written response to this 

report within 90 calendar days of the date of this report. You should include a corrective action 

plan for agreed upon actions, including milestone dates. We have no objections to the further 

release of this report to the public. This report will be available at http://www.epa.gov/oig. In 

addition to providing a written response, please e-mail an electronic version to 

Brass.Ira@epa.gov. 

If you or your staff have any questions regarding this report, please contact me at 

(202) 566-0830 or Ira Brass at (212) 637-3057. 
Table of Contents

At a Glance 

Chapters 

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

Purpose .......................................................... 1

Background ....................................................... 1

Scope and Methodology ............................................. 5

Results in Brief ..................................................... 6

2 Management of Backlog Improving, But Challenges Continue ........ 7

EPA and States Have Been Addressing Challenges, 

But Further Action Can be Taken ................................... 7

EPA Increasing Focus on Environmental Outcomes for

Permit Issuance and Program Management .......................... 15

Agency Comment and OIG Evaluation .................................. 16

3 Environmental Impacts of Backlog Reduction

Vary and May Be Limited ....................................... 18

Backlogged Permits Do Not Appear to Be a Major Cause of Impairment ........ 18

Delays in Reissuing Permits May Have Varying Environmental Impacts ........ 20

Environmental Significance of Backlog Could Increase in Future .............. 22

EPA Should Continue Promoting Prioritization of Permit Issuance ............ 25

Agency Comment and OIG Evaluation .................................. 26

4 Backlog Reporting Has Provided Inadequate Measure

of Environmental Results ....................................... 28

Improvements in Backlog Measurement Affected Reported Progress .......... 28

Backlog Measure Has Not Reflected Environmental Outcomes ............... 36

Agency Comment and OIG Evaluation .................................. 41

5 EPA Can Take Various Actions to Reduce 

NPDES Permit Backlog and Improve Water Quality ................. 44

EPA’s Management of NPDES Backlog Highlights

Importance of an Integrated Clean Water Program ..................... 44

EPA’s Steps to Improve Program Integration Need to Be Strengthened ........ 46

Recommendations .................................................. 46

Agency Comment and OIG Evaluation .................................. 49

i 
Appendices 

A Details on Scope and Methodology .............................. 53

B Definitions and Examples of Alternatives to General Permitting ...... 57

C Changes in Permit Limits ...................................... 58

D Factors That Indicate a Permit Likely to Have 

New Limits or Conditions When Reissued ......................... 59

E Universe of Permits Counted in Backlog

and Number of Current Permits ................................. 60

F Agency Comment ............................................ 61

G Distribution .................................................. 80

ii 
Chapter 1

Introduction 

Purpose 

National Pollutant Discharge Elimination System (NPDES) permits provide a 

regulatory approach for controlling point source discharges to surface waters. 

The Agency first reported the backlog as a material weakness for the NPDES 

program, then tracked it internally as an Agency weakness after October 2002. 

Expired NPDES permits may not incorporate the most up-to-date limits and 

conditions to protect human health and aquatic life, thereby delaying needed 

improvements in water quality. The Office of Inspector General (OIG) has issued 

two previous reports on issues relating to the backlog and reported it as an OIG 

Management Challenge until 2005. For this current report, we evaluated the 

following questions: 

• How successful have EPA and the States been at managing the backlog? 

• What is the potential for environmental impact of the NPDES permit backlog, 

including impacts on loadings reductions? 

• How well does the NPDES permit backlog measure (percentage of major and 

minor permits backlogged) reflect environmental impacts of delayed permit 

reissuance or issuance? 

During our work, we also collected information on successful regional and State 

practices that might be useful for others. 

Background 

Permit Program Established 

Congress established the NPDES program through the 1972 amendments to the 

Federal Water Pollution Control Act. NPDES permits regulate discharges from 

point sources (discharging through a discrete conveyance for water, such as a pipe 

or man-made ditch) through enforceable provisions designed to reduce the 

discharge of pollutants to surface waters to protect and improve water quality. 

NPDES permits are issued to a variety of dischargers and can be categorized by 

type of discharge regulated, facility, and permit. The permit program originally 

focused on municipal Publicly Owned Treatment Works and non-municipal 

(industrial) facilities, but has been expanding to include stormwater, combined 

and sanitary sewer overflows, Concentrated Animal Feeding Operations 

(CAFOs), and sludge (biosolids). 

1 
EPA manages permits through two designations – major or minor permits – as 

shown in Table 1.1: 

Table 1.1: Permit Designations 

Type Description 

Majors Publicly Owned Treatment Works having discharges greater than 1 million gallons 

per day or serving a population of 10,000 or more, industrial facilities scoring over 80 

points based on rating criteria, and a limited number of discretionary majors (facilities 

not meeting the above criteria but designated majors by States). 

Minors Publicly Owned Treatment Works of less than 1 million gallons per day, and industrial 

facilities that fail to meet the criteria score of 80. 

Individual permits are those issued to a single facility, while a general permit will 

result in multiple facilities within a specific category and geographic area being 

covered under one permit. In June 2003, according to EPA’s status reports, the 

total universe of facilities reviewed for backlog accounting purposes within the 

NPDES program was 6,675 major permits (including at least 48 general majors), 

45,419 individual minor permits, and 50,587 general non-stormwater permitted 

minor facilities. In July 1999, EPA had estimated that Phases I and II of the 

National Storm Water Program would add about 400,000 facilities for general 

permit coverage, but general stormwater permits are excluded from the backlog 

definition. 

Permits, the result of a regulatory process, consist of general and specific 

conditions, enforceable limits, and monitoring and reporting requirements. 

Permit limits are generally based on the more stringent limit calculated using a 

water quality standard, an effluent guideline (a technologically based standard), or 

in some cases best professional judgment. However, if the receiving waterbody 

has been assessed as impaired, a study is conducted to derive the Total Maximum 

Daily Load (TMDL) – the maximum amount of a pollutant the waterbody can 

receive and still meet water quality standards. Waste Load Allocations (WLAs) 

allocate discharge allowances within the TMDL to point sources and are 

incorporated in an NPDES permit to provide the discharge limit for that pollutant. 

A flowchart depicting the NPDES permit process based on our project work is 

provided in Figure 1. 

2 
Figure 1: Stylized Flowchart of NPDES Permits and Other CWA programs Designed to Achieve Water Quality Goals 

pretreatment 

standards 

Shaded objects are not directly affected by the NPDES permit 

1) Effluent Guidelines includes technology standards that address secondary preatment in POTWs as well as Best Professional Judgment limits. 

2) Watershed permitting may also affect the process. This approach is shown for illustration only and may be implemented differently than shown. 

Note model does not show: monitoring, reporting, or 

enforcement 

Technology 

Standards (Effluent 

Guidelines) (1) 

Water Quality 

Standards 

NPDES Permit 

(limits) 

Regulated 

Discharger 

water 

quality 

changes 

Waste Load 

Allocation 

Load

 Allocation 

Unregulated 

Discharger 

(Nonpoint 

Source) 

Effluent Trading 

Program (2) 

permit limit 

compliance 

Best 

Management 

Practices 

(BMPs) 

POTW 

with 

pretreatment 

Indirect 

Industrial 

Discharger 

BMP implementation 

& maintenance 

local limits 

pollutant 

discharge 

changes 

Total Maximum Daily 

Load (TMDL) 

Authority for the NPDES program is currently delegated to 45 States. In these 

States, most permits are issued by the State, and major permits (or a selection) are 

reviewed by the EPA region. EPA can issue a permit in authorized States directly 

if a State does not address objections raised by EPA where the permit conflicts 

with Federal requirements. In the remaining five non-delegated States, EPA 

regions are the permitting authority and issue the permits. The Permit 

Compliance System (PCS) is the data base for NPDES reporting, and includes 

tracking for major facilities. PCS data for minors is not as complete as for 

majors. 

Two efforts are currently underway that address the permitting program and 

impact the backlog. The Office of Wastewater Management believes that 

ongoing efforts led by the Office of Enforcement and Compliance Assurance to 

modernize the PCS system will help all aspects of permit program management, 

including permit issuance. In anticipation of the modernized system, EPA is 

revising the existing PCS policy to require permit event data to be recorded for all 

3 
facilities. However, the modernization effort has encountered delays. The Office 

of Wastewater Management has also developed and begun implementing the 

“Permitting for Environmental Results” (PER) Strategy that has three primary 

components addressing program results, efficiency, and integrity. Office of 

Wastewater Management emphasizes the importance of this strategy in managing 

the overall NPDES permit program’s effectiveness. 

Backlog of Expired Permits Identified 

Under Federal regulations, permits may be issued for a period of no more than 

5 years. Permits for new applications must be issued prior to a facility beginning 

to discharge. Once issued, a permittee submits an application to renew NPDES 

permits prior to expiration. If the application is received but the new permit is not 

issued prior to expiration, the expired permit is administratively continued and 

enforceable until a new permit is issued.1 However, expired permits may not be 

modified. Based on the various inputs, EPA states that permit renewals have the 

potential to affect water quality in a number of ways, including more stringent 

technology-based limits for existing permits, limits on new parameters, water 

quality-based limits, whole effluent toxicity limits, best management practices, 

and improved monitoring requirements. 

A large number of NPDES permits were expired and not reissued on a timely 

basis and became known as the “permit backlog.” EPA tracked the backlog as a 

Federal Managers’ Financial Integrity Act material weakness from 1998 to 2002, 

and downgraded the issue to an Agency level weakness and reported it as 

corrected in 2003. 

EPA developed the Permit Issuance Framework in 1999 to provide interim 

management of the NPDES permit backlog. This document discusses causes of 

the backlog and goals, and provides a description of strategic initiatives for 

reducing the backlog. There are descriptions, desired outcomes, and short- and 

long-term actions developed for each of the following four initiatives:

 1. Understand and better define the backlog.

 2. Examine permitting efficiencies and facilitate programmatic and technical 

streamlining opportunities.

 3. Provide funding and technical support for regions and States.

 4. Encourage regions and States to share technical expertise and permitting

tools.

1 An environmental group has filed a legal challenge regarding a facility in Hawaii having its NPDES 

permit administratively continued. 

4 
Through the recently adopted PER Strategy, EPA is also now providing for a 

prioritization approach for addressing backlogged permits, focusing on 

environmental results. 

EPA defines and reports on the backlog through a measure based on the 

expiration date in PCS, including what types of permits and how long after 

expiration a permit will be considered backlogged. In its Federal Managers’ 

Financial Integrity Act reporting, EPA recognized the need to clean up the data 

and process for tracking the backlog to provide a more accurate picture of the 

universe of permits. As backlog management evolved, EPA also reached 

consensus with permitting authorities to include non-stormwater general permits 

in the backlog inventory. The definition of the backlog has changed over time; in 

June 2003, the backlog definition included individual and generally permitted 

major facilities (including individual stormwater permits) and individually and 

generally permitted minor facilities with standard permits (designated CAFO, 

stormwater, or biosolids permits not counted). Individual permits awaiting 

reissuance are considered backlogged after 180 days; generally permitted nonstormwater facilities, permit applications, and permits missing expiration dates 

are considered backlogged immediately upon entry into PCS. 

As of June 2003, out of the potential universe described above, the backlog was 

reported as consisting of 1,120 major, 9,386 individual minor, and 6,512 general 

minor nonstormwater facilities. 

Scope and Methodology 

We conducted our field work from August 2003 to July 2004 in accordance with 

Government Auditing Standards, issued by the Comptroller General of the United 

States. We focused on the national backlog of permits in the NPDES program as 

defined by EPA from November 1998 through March 2004. We limited the 

review to backlog issues and only addressed overall programmatic issues; permit 

quality issues, and compliance and enforcement issues (including the issue of 

potentially expired versus administratively continued backlogged permits) were 

outside of the scope of this study. While addressing the backlog measure in terms 

of managing the program, impacts on perceptions of permittees or others 

regarding program management were not addressed in this study. Our review 

involved all EPA regions and Headquarters, as well as 15 States. During this 

project, we conducted literature reviews, interviewed State and EPA officials, 

made site visits, and obtained data through three separate surveys. Data from 

PCS and other EPA data systems were also used to analyze the permit backlog. 

The OIG has issued several reports addressing issues related to the NPDES permit 

program, and issues raised in those reports, as well as various other studies, were 

taken into account during our review. Details on our scope and methodology, 

including the prior reports considered, are in Appendix A. 

5 
While this report addresses a number of programmatic issues, it focuses on the 

backlog of permits within the NPDES program. We limited our work according 

to EPA’s definition of the backlog, which encompassed a subset of the NPDES 

permitting universe. While we addressed overall programmatic changes that 

affected backlog management, our work did not include a complete review of the 

NPDES program or the PER Strategy that EPA has been using since 2004 to 

manage the NPDES program. 

Results in Brief 

EPA and the States have had varying success in eliminating the backlog of 

NPDES permits requiring renewal, and more still needs to be done. The NPDES 

permit program is only one of many EPA programs to improve surface water 

quality. EPA needs to integrate its efforts to eliminate the NPDES backlog with 

those other programs. 

As discussed in Chapter 2, EPA needs to address challenges involving resources, 

workload, permit complexity, external sources of delay, and oversight. In 

Chapter 3, we note that only a small portion of waters currently identified as 

“impaired” are associated with backlogged permits, and EPA needs to prioritize 

its efforts to allocate permit writing resources based on the greatest potential 

environmental benefits. Chapter 4 discusses how reporting on the backlog 

measure under the Government Performance and Results Act did not provide an 

accurate view of the program status or an adequate measure of environmental 

results. Chapter 5 summarizes our overall conclusions and recommendations. 

EPA has been taking various actions to address the NPDES permit backlog, and 

needs to build on those steps already initiated. EPA is now managing the NPDES 

permit program through the PER Strategy, designed to increase focus on 

environmental outcomes. We encourage EPA to continue refining this strategy. 

In a March 2005 response to the draft report, EPA provided extensive comments 

in response to our draft report. We summarized EPA comments, along with our 

evaluation of those comments, at the end of Chapters 2 through 5. EPA 

comments are reproduced in Appendix F. 

6 
Chapter 2

Management of Backlog Improving, 

But Challenges Continue 

EPA and the States have employed different approaches with varying success in 

reducing the backlog of NPDES permits. The Clean Water Act requires that 

NPDES permits be renewed at least every 5 years. To reduce the backlog of 

permits requiring renewal, several challenges need to be addressed, including: 

• Resource constraints 

• Increasing workload 

• Increasingly complex permitting issues 

• External sources of permitting delays 

• Communication/oversight limitations 

EPA and State efforts have helped reduce the backlog through a variety of 

strategies, including permitting efficiencies. Additional management approaches 

have included focusing on significant permits. Questions remain as to whether 

backlog reduction will be maintained. Additional efforts are underway to address 

ongoing and new challenges. In 2004, EPA began implementing a PER Strategy 

that will help focus permitting efforts on environmentally significant permits. 

EPA and States Have Been Addressing Challenges, But Further 

Action Can be Taken 

This chapter deals with causes of the NPDES permit backlog, and management 

strategies and tools for better managing the backlog. EPA still needs to further 

address resource constraints, increasing workload, complex permitting issues, 

external sources of delays, and communication/oversight limitations. Chapter 3 

discusses the potential environmental impact of permit backlog reduction, and 

how environmental significance is critical in making decisions on which permits 

should be addressed first. Chapter 4 addresses measures and administrative 

changes that may have an impact. 

Resource Constraints Continue to Hamper Efforts 

Budget limitations continue to strain many States’ abilities to meet permitting 

goals. Six of the 7 States and 2 of the 10 Regions surveyed regarding causes of 

the backlog indicated this concern. A second survey indicated resource 

constraints will continue to affect backlog management. Further, in a 2002 report, 

the National Academy of Public Administration found the resource gap between 

State expenditures and resource needs was approximately $0.7 to $1 billion for 

Clean Water Act programs. The Academy expects substantial additional State 

7 
efforts will be necessary due to incorporating TMDL-based limits in permits, 

since this likely will result in increased public involvement, more resistance from 

applicants, and the use of such innovative approaches as pollutant trading. 

Regions and States have undertaken a number of strategies to address resource 

constraints. Following are some strategies implemented or being considered for 

addressing resource issues: 

• Ohio had permit writers work on simple (single-discharger) WLAs while 

expert modelers focused on TMDLs and other complex models. This allowed 

simple allocations to be performed more promptly. 

• Minnesota used staff work plans to better monitor productivity for permit 

issuance timeliness, number of permits expected, timeliness of establishing 

effluent limits, and other landmarks. 

• Indiana is considering overtime, reprogramming funds (with EPA assistance) 

to pursue use of Senior Environmental Employee Position employees, shifting 

employees on a part-time basis, trying to identify financial resources from 

other areas (such as shifting Federal air funds), filling non-permit vacancies, 

and identifying special assistance to address resource issues. 

• Illinois recently authorized a system for collecting permit fees, and Michigan 

was counting on fees to replace half the general fund. 

• Region 10 had a 3-year plan for issuing permits. The plan describes goals for 

the program and a schedule to meet supporting objectives, including backlog 

goals; addresses disinvestments; and has a permit selection process, including 

priority criteria, and a two-tier priority workload list for permits to be issued. 

• Region 8 provided Colorado with contractor assistance, through a national 

contract, to eliminate its majors backlog. (Four regions identified the use of 

contractor assistance as a particularly successful practice.) 

There are potential drawbacks or challenges for some of these strategies, 

including impacts on commitments in other programs due to shifting resources 

(e.g., lower achievements for the other programs), and the amount of training 

needed for part-time or temporary reassignments. 

 Workload Management Approaches Had Varying Success 

EPA’s and States’ Clean Water permitting programs have been facing a growing 

workload. In addition to issuing NPDES permits for traditional point sources 

reflected in the backlog measure, they are responsible for other duties and permits 

(e.g., stormwater, CAFOs, biosolids, and State-specific non-NPDES permits). 

Some of these other classes of permittees have been growing dramatically. EPA 

8 
and States have used different permit workload management approaches and 

efficiencies with varying success. We identified two categories of approaches: 

(1) overall permit management and prioritization of reissuance, and (2) adoption 

of tools to increase efficiency. 

Permitting Strategies Address Both Overall Workload and Backlog 

EPA and States have devised general workload management approaches to 

address the increasing workload. These strategies are designed to improve 

permitting efficiency and decrease the size of the backlog, or to target their efforts 

toward permits or categories of permits of interest. These approaches typically 

group permits according to some common factor, such as location, time in the 

backlog, or facility type. 

Permitting According to Rotating Basins: Permitting according to a “rotating 

basin” approach uses the natural boundaries of a watershed, basin, or sub-basin to 

define groups of permits for permitting and manage other clean water functions. 

Regions identified various approaches at the State level that were successful. 

Approaches vary among States. For example: 

• Michigan manages non-contiguous sub-basins across the State to balance the 

workload. Each year, all permits scheduled to be addressed that year expire at 

the beginning of the year, allowing Michigan to work on multiple related 

permits as needed. 

• North Carolina uses sub-basins to manage permitting and may divide these 

sub-basins to even out workloads as necessary. In general, a different basin is 

permitted each month. 

However, one of the key barriers previously identified by States to issuing all 

permits within a specific basin was an uneven permitting workload across basins 

and special Federal initiatives that divert resources from basin permitting cycles 

(e.g., EPA permit backlog strategy). Some States abandoned a rotating basin/ 

watershed approach after it drove up their backlog or have not adopted it despite 

considering it. 

Prioritizing Within an Overarching Approach or as an Independent Strategy: 

Prioritizing permits can be particularly useful to accomplish environmental or 

other management goals where 100-percent permit coverage is unlikely. Permits 

are being prioritized for issuance by a number of different approaches and factors, 

including the rotating watershed/basin approach, backlog reduction, being a major 

permit, being a new permit, and enforcement issues. Regions also indicated that 

while a number of States are not using human health or environmental factors for 

prioritizing permits for reissuance, a number are, including such factors as: 

downstream drinking water sources, upstream of likely human exposure, 

endangered species, permit likely to have changes, and toxic discharges. 

9 
Examples of different prioritization approaches are highlighted below: 

• New York established the Environmental Benefit Permit Strategy in 1994 that 

consists of a permit renewal process (see Chapter 4) and a formal permit 

prioritization process. The prioritization process scores and ranks majors and 

significant minor permits using 13 priority ranking factors. 

• Region 10 developed a database to assist in prioritizing permitting efforts 

according to established criteria: priority, tribal, and general permit criteria. 

Priority criteria included elements such as permit facilities in the oil and gas, 

mining, and food packing industries; new sources; and high profile facilities. 

• Region 3 developed a prioritization tool – called the “Daunting Dozen” – to 

focus efforts on the oldest backlogged majors in the region. 

• North Carolina prioritizes permits by identifying those minor facilities that 

will not need significant changes or resources, and “expediting” these through 

issuance by staff that are new or generally have less technical experience. 

They assign more difficult permits to experienced permit writers. 

• Washington has permit priority ranking criteria and has also been continuing 

to adjust its process in identifying permits with little or no changes eligible for 

reauthorization. 

Tools and Efficiencies May Increase Permit Coverage 

EPA and States have developed or are considering permitting tools and 

efficiencies for improving permit issuance rates. Several have been successful, 

while others have potential risks, limitations, or drawbacks. 

Reducing Certain Activities May Reduce Workload: States may reduce 

activities that are outside of backlog accounting in order to focus permitting 

resources on management of the backlog. These activities include permitting of 

non-NPDES permits, making certain types of modifications a lower priority, or 

not pre-reviewing applications. Minnesota has a Customer Assistance Center that 

handles routine questions not requiring a permit writer to respond. However, 

some States have stopped doing all or part of required PCS data entry, which can 

result in PCS not providing accurate oversight data. Also, 7 of the 8 States 

responding to our questionnaire and 7 of the 10 EPA regions indicated it would be 

helpful in reducing the backlog if permits did not have to be reissued as 

frequently. However, since the 5-year permit term is dictated by the Clean Water 

Act, making a change would require an Act of Congress. 

Alternatives to Traditional Individual Permitting Can Increase Efficiency: 

Individual permitting alternatives, such as general permits, can increase efficiency 

by consolidating similar facilities under one permit. A general permit covers 

10 
multiple facilities within a specific category and geographic area (e.g., county, 

State). As of March 2004, about half of the facilities eligible for consideration 

under the backlog definition were covered by general permits. Specifically, out 

of a total of 100,261 facilities, 48 major facilities in Region 10 and 51,382 minor 

facilities nationwide are covered by general permits. However, although a greater 

utilization of general permits offers significant efficiency opportunities, there can 

be limitations and drawbacks. For example: 

• Not all facilities in a State are likely to be appropriate for general permit 

coverage, and it may also not be appropriate for all facilities in a general 

category to be covered by a general permit. 

• There may be insufficient resources available to take advantage of general 

permitting. 

• If a single general permit expires and becomes backlogged there is the 

potential to see a large increase in the State’s backlogged facilities. 

• General Statewide permits may need to be managed independently in 

conjunction with a rotating basin management. For example, a general 

Statewide permit would likely permit facilities that would normally be 

associated with different basin permitting cycles. EPA commented that 

Michigan has indicated they are experiencing a lot of success with this hybrid 

approach. However, if general permits are issued on a per basin basis, this 

may require issuance of more than one general permit and processing of 

notices of intent at different time periods. 

• General permit data is not captured well in the current PCS system, hampering 

oversight. 

Apart from general permits, States are also using non-traditional approaches to 

issue permits, such as permits by rule, cookie-cutter permits, rollover permits, 

reauthorized permits, reduced effort permits, expedited permits, and batch 

permitting (see Appendix B for descriptions). In general, these approaches help 

to manage workload by grouping permits of similar types, needing less work or 

revision. 

Electronic Tools Present Opportunities: States and regions believe that 

automating permitting tasks, with tools such as electronic permitting and tracking 

as well as automating data entry, can improve permit issuance rates. Eight of 10 

regions also indicated they would like EPA assistance in the area of electronic 

signatures to enable electronic permitting and Discharge Monitoring Reports. 

EPA and States have developed a number of electronic tools. For example: 

11 
• Mississippi’s backlog decreased from 20 percent in October 2002 to 7 percent 

in September 2003 by using “Ensite” – an in-house computer software 

program – to increase permit writing efficiency. 

• Michigan has a computerized NPDES Management System with several 

integrated electronic functions (including application logging and tracking, 

permit writing, public noticing, communication with supporting units, and 

updating PCS), resulting in such savings as reduced staff time for data entry. 

However, although promising, transitioning to a new data system can have 

significant short-term costs. For example, Kentucky’s permit backlog has 

increased, and the State attributes the existing increase in its backlog in part to the 

time and resources spent to transition to and maintain a new management system. 

Continuing challenges with system functionality have led to additional permit 

processing delays as well as shifts in staff resources. 

EPA states that it is increasing outreach efforts regarding electronic tools in 2005. 

EPA established a Clean Water Act 104(b)(3) cooperative agreement with the 

Association of State and Interstate Water Pollution Control Administrators 

(ASIWPCA) to collect and share good strategies and practices among States as 

well as participate in the PER process. 

Headquarters Initiated Tools for Addressing the Backlog: EPA Headquarters 

had proposed or introduced a number of permitting tools, although some regions 

indicated they were unaware of some of them. Additional tools are under 

development While there were some criticisms regarding time or resource 

requirements, regions generally provided positive comments, indicating the 

various tools contributed to benefits such as consistent high quality permits, 

increased permit efficiency, and reduced burdens. Examples of tools include: 

• A permit quality review checklist 

• Permit Application Software System (e-PASS) for electronic applications 

• Central Tenets of the NPDES Program 

• The electronic Permit Issuance Forecasting Tool (ePIFT) 

• NPDES permit writer training 

• Internet accessible NPDES permits 

• A permit prioritization checklist (criteria for identifying high priority permits) 

As an outcome of the PER process, EPA also expects to be able to identify 

opportunities to further assist permitting authorities. 

 States and EPA Must Address Increasing Complexities 

While EPA has been addressing the increasing complexity of writing permits, it 

needs to continue exploring ways to efficiently address this issue. Most States 

and regions responding to our survey identified permit complexity as a significant 

12 
contributor to the June 2003 backlog. They cited the increasing complexity of the 

permit process and increasing sophistication of facilities, third parties, and new or 

revised regulations. Adding complexity is the inclusion of limits calculated using 

TMDL methodologies, new water quality standards, new or revised effluent 

guidelines, and requirements of new or additional studies. Following are 

examples of steps taken to address complexity: 

• EPA noted that short term modifications of standards through variances 

provide more time to fully study an issue. For example, Region 5 submitted 

information that “Ohio has a group variance for mercury that has made the 

stringent new water quality standards essentially a non-issue in permit 

renewals.” 

• There has been some coordination of information development across 

programs that could reduce the time and resources needed to develop data for 

permitting. Two examples are Colorado’s coordination of permit drafting 

with the Assessment unit, and Region 7 working with States to coordinate 

TMDL and permit schedules to promptly address the most significant issues. 

EPA also highlighted North Carolina’s rotating basins program, indicating 

there has been a good use of linkages. 

• Region 3 identified as a successful practice the use of a team of EPA and State 

staff to address the oldest backlogged major permit in the region, along with 

assistance from EPA Headquarters and national experts in the industry. Eight 

of 10 EPA regions indicated they want more technical support for permit 

issuance from EPA.

 External Backlog Causes Present Difficulties 

While individually a number of external causes of the backlog were not 

considered to be a significant source of delay, collectively, several States and 

regions noted they can be a significant problem. External causes involved 

permitted facilities and third parties. Examples of actions taken follow. 

Applications: Some permitting authorities cited delays related to submission of 

applications less than 180 days prior to expiration or applications that are 

incomplete as a significant cause of the backlog. Reminder letters can be sent out 

about a year prior to permit expiration to request timely submittal of permit 

applications for permit reissuance. One State issues penalties for permits that 

expire due to late applications. Region 5 indicated that in Minnesota, central 

review of applications helped ensure that only complete applications were sent to 

permit writers. 

Comments on draft or final permits: Public comments and hearings on permits 

are an important part of the process but can lead to delays in permit issuance. 

Some permitting authorities are focusing on increased public communications to 

13 
address these delays. EPA has begun posting major permits on the Internet. 

Some permit authorities are bundling public notices, although if hearings are 

requested delays could still occur. Michigan has improved public information by 

providing Internet access to all public notices and fact sheets for proposed 

permitting actions, access to electronic NPDES permit application forms, and 

listing of new and reissued general permits. 

Required consultations, in addition to public comments: Certain actions require 

consultations with other Federal agencies, State organizations, or tribes, and 

efforts have been made to make consultations more efficient. Region 6 has been 

working more with States to improve the 401 certification process. A permit 

quality review checklist has been developed to increase likelihood of an 

approvable permit by EPA, but while a modified tool is used in some Region 3 

States we did not find any other implementation. EPA Region 10 indicated that 

additional outreach and technical assistance (explaining EPA’s permitting 

process to tribes and the Fish and Wildlife Service) could reduce consultation 

time on permits. 

Permit limit calculations delayed due to delayed or expected WLAs, water 

quality standards, or effluent guidelines: Permit limits are largely derived using 

outputs from other programs, such as the water quality standards, effluent 

guidelines, and TMDL programs. However, delays in these programs can cause 

delays in reissuing permits. Permitting authorities may hold up issuing permits 

when there are pending TMDLs or water quality standards. The use of reopener 

clauses has allowed some permitting authorities to reissue permits without 

potentially delaying incorporation of WLAs until the next time the permit is 

reissued (possibly by up to 5 years). EPA has stated it will be working to reduce 

the water quality standards backlog that has delayed some new water quality 

standards. Permitting authorities surveyed regarding causes of the 2003 backlog 

generally indicated that permits were not being held up due to pending revision of 

effluent guidelines. However, in some cases, old, missing or outdated effluent 

guidelines have presented a problem for a State. The State may make complex 

engineering determinations to replace the effluent guidelines, and challenges may 

arise due to the reissued permits being more stringent than those which would be 

calculated using the older national guidelines. 

Opportunities Exist for Improved Communication 

EPA has taken a number of steps to improve communication to better address the 

backlog. However, additional efforts to increase communication could lead to 

further improvements in permit management and reducing the backlog. 

EPA reports using a number of channels for communication such as: monthly 

calls and meetings with States through ASIWPCA; training and practitioner 

meetings for permit writers; a comprehensive Web site with additional training in 

14 
specific program areas; and periodic meetings between States and EPA regions, 

including State program reviews by regions. 

There has been no annual meeting for surface water permitting as there is for 

other programs, such as pretreatment, TMDLs, and biosolids. A national 

permitting forum would be a way for all States and regions to work together to 

identify inconsistencies and address issues. EPA indicates a National Meeting 

with States and regional NPDES managers is planned for September 2005. 

EPA has been working with organizations like ASIWPCA to have a better 

exchange of information with States. EPA regions are also working with States to 

improve NPDES permit backlog management. For example, in Region 5, the 

Streamlining Workgroup captured State challenges, proposed solutions for 

various levels of government, and provided a forum to exchange information on 

positive experiences. 

While EPA maintains a potentially valuable NPDES backlog Web site with 

postings of backlog status reports and other background information, several 

States contacted were unaware about the availability of information. For 

example, one State was not aware of EPA’s adjustment of the backlog time period 

to 180 days after expiration. 

EPA Increasing Focus on Environmental Outcomes for 

Permit Issuance and Program Management 

Eliminating or managing the backlog is just one element of water quality 

management and the NPDES program. Potential environmental impacts of 

permitting and the backlog are described in Chapter 3. In the 1999 Guidance 

document, EPA outlined strategic initiatives and a multi-step process of shortand long-term actions for managing the NPDES permit backlog. EPA has been 

developing and implementing the PER Strategy, which consists of three primary 

components, described by EPA as: 

• Program Results - To maximize benefits, permits will be prioritized by 

identifying environmentally significant permits within and among watersheds. 

This element requires identification of data to characterize the universe and a 

screening checklist. 

• Program Efficiency - Best practices will be identified and shared to increase 

efficiencies. EPA will document research on current practices and legal 

authorities as well as provide support and technical assistance. 

• Program Integrity - Tools will be used to continually assess program 

performance and ensure continued success. EPA is developing selfassessment questionnaires, a management report providing a snapshot of State 

performance over four areas, and State NPDES program profiles to be used in 

15 
conjunction with the other tools. EPA is developing performance assessment 

and feedback mechanisms as well as updating NPDES program oversight 

guidance. 

EPA continues to refine and develop this strategy, which contains a 

Communication and Outreach element addressing training, outreach, and 

communication, and a cooperative agreement with ASIWPCA for a workgroup as 

well as regional liaisons. EPA has been actively collecting State data and using 

information to develop publicly available State profiles, and has also been 

developing NPDES management reports for the program’s performance. 

* * * 

Conclusions and recommendations for this chapter are in Chapter 5, where they 

are integrated with conclusions and recommendations from other chapters. 

Agency Comment and OIG Evaluation 

EPA provided additional information and recommendations for clarifications to 

this chapter of the draft report. We have made revisions as appropriate to reflect 

this information. 

EPA also stated in its comment that beginning in 2004, the PER Strategy 

establishes a new vision for managing the NPDES program using the PER 

Strategy's elements: integrity, efficiency, and environmental results. EPA 

requested that the report emphasize the role of implementation of the PER 

Strategy in addressing overall permit program effectiveness, particularly with 

respect to water quality improvements. We have added discussion of PER in 

several places to give EPA credit for actions taken. It should be noted that PER is 

a new approach designed to address a number of the causes of the backlog. The 

discussion of causes and strategies provides more historic information, and since 

PER was only recently implemented (in 2004), we expect it will have more 

significant impact in the future. 

EPA also concurred with the OIG’s assessment that resource constraints hamper a 

permitting authority's ability to meet permitting goals. EPA said that declining 

State resources are one of the most problematic issues facing permitting 

authorities. In addition, EPA commented that, as noted in the report, many 

permitting authorities have stepped up to the challenge using various approaches 

to increase efficiencies. 

As is discussed in Chapter 3 in more detail, we generally agree with EPA’s 

comment that incorporating new or revised effluent guidelines in permits that 

have been backlogged should be a priority, as is reflected by EPA’s identification 

of this issue as a prioritization factor. However, the survey responses indicated 

that permits were not being backlogged to wait for the revision or promulgation of 

16 
an effluent guideline. Therefore, although EPA indicates incorporating effluent 

guidelines in a permit that is 15 years old is important, this is a different issue 

than anticipation of a new or revised guideline being the cause of a permit being 

in the backlog. Therefore, we did not modify the discussion of the significance of 

waiting for new or revised effluent guidelines as a cause of the backlog. 

17 
Chapter 3

Environmental Impacts of Backlog Reduction 

Vary and May Be Limited 

The overall environmental impact of the NPDES permit backlog has been limited, 

but there is variability across permits. Backlogged permits are associated with 

only a small portion of waters currently identified as being “impaired.” Further, 

while the majority of backlogged permits when renewed had changes to their 

discharge limits and a large number of the new permits contained limits for new 

parameters, the majority of the controls in the prior permits did not change and 

facilities were often already in compliance with the new limits that were 

reviewed. This suggests that EPA's recent steps to prioritize permitting resources 

according to potential environmental impact are on the right track as long as EPA 

obtains needed information. Although the significance of the backlog has been 

limited in the past, it could grow as a result of increased efforts in other water 

protection programs that may necessitate NPDES permit revisions. 

Backlogged Permits Do Not Appear to Be a Major Cause of 

Impairment 

A critical question about the NPDES permit backlog is how large of a role 

backlogged permits have played in delaying the achievement of clean water goals. 

Based on our review of available data, the backlog has played only a minor role in 

impairing waters. Our analysis indicated that backlogged permits affected only a 

very small portion of the 26,209 State-identified impaired waters (reported in 

EPA’s April 2004 303(d) fact sheet). We were not able to precisely quantify the 

relationship of backlogged permits to impaired waters (the likelihood of a water 

being impaired if a discharging facility had a backlogged permit) due to several 

methodological issues. Therefore, directly linking impacts of backlogged permits 

to impaired waters was not possible in this study for several reasons, including: 

• Waters listed as unimpaired that are actually unassessed; although we have 

not assessed it, a web-link for access to this type of data has been added to the 

WATERS database. 

• Not all permits being georeferenced (although these are known). 

• Difficulties in determining whether the pollutant of concern is discharged by 

the permitted facility because it may not match PCS parameters. 

• Variation among State water quality standards, percent of waters assessed, 

and 303(d) listing process between States. 

However, analysis of existing best-available data provides support for the 

conclusion that individual backlogged permits play a limited role in known 

impaired waters. NPDES permit pollution sources (point sources) are not 

18 
believed to be the primary source of water quality impairments. In FY 2002,2 

EPA estimated generally that about: 

• 10 percent of waters (approximately 2,600) were impaired solely due to point 

sources. 

• 50 percent (approximately 13,000) were due to a combination of point and 

nonpoint sources. 

• 40 percent were impaired only by nonpoint sources. 

The greater estimated nonpoint source contributions (associated with 90 percent 

of impaired waters compared to 60 percent of impaired waters associated with 

point source) are due to a certain extent to the large number of successes in 

limiting point source pollution as a result of the Clean Water Act. Over 10 years 

ago, in 1993 guidance, EPA stated that, “the majority of the remaining water 

quality impairments ... result from nonpoint source pollution and other 

nontraditional sources....” More recently, EPA's FY 2005 National Water 

Program Guidance states that nonpoint source pollution (and other nontraditional 

sources), addressed under Section 319 of the Clean Water Act, is the largest 

single cause of water pollution. In its response to our draft report, EPA stated that 

conclusions cannot be made regarding impacts of point source contributions until 

TMDLs involving point sources are completed. However, EPA FY 2002 training 

material stated that it was also likely that “in many of the 50 percent of the 

impaired waters where both point and nonpoint sources are significant 

contributors, nonpoint sources contribute considerably more pollutant loads than 

do point sources” (see footnote 2 for citation). While we do not recommend 

drawing water- or facility-specific conclusions from the data at this point, 

available information suggests that backlogged permit impacts should be 

considered within both the context of point source and nonpoint source 

contributions to impaired waters. 

In terms of overall causes of impaired waters, the permit backlog is limited. While 

we could not describe a relationship between the status of permits as backlogged 

and the likelihood of waters being impaired, we analyzed three EPA data sets that 

matched NPDES permits to impaired waters to look at the relative association of 

backlogged permits to known impaired waters. While two of the data sets are 

preliminary and all draw from PCS data that contain some locational data gaps, 

we found a small number of impaired waters (ranging from approximately 3 to 14 

percent) appear to be associated with backlogged permits (see Appendix A for 

description and methodology). This supports our general conclusions based on an 

estimated 60 percent of impaired waters likely to be affected by point sources, 

2

 Clean Water Act Module, Watershed Academy. See http://www.epa.gov/watertrain/cwa/cwa28.htm 

(last updated October 28, 2002) and http://www.epa.gov/watertrain/cwa/right52.htm (last updated March 12, 2003). 

More recent figures show: 10% point sources only; 43% nonpoint sources only; 47% combination of point and 

nonpoint sources for 1998 303(d) list – see http://www.epa.gov/owow/tmdl/tptmdl (last updated February 16, 2005). 

19 
and the backlog of permits now being less than 20 percent of the traditional 

NPDES universe. 

Delays in Reissuing Permits May Have Varying Environmental 

Impacts 

Analysis of data from a large subset of previously backlogged major permits 

indicate that delays in permit reissuance can have varied environmental impacts. 

When the backlog was identified as a material weakness and management 

challenge, while reissuance of permits was valuable for a number of reasons, an 

overriding concern was that expired NPDES permits may not incorporate the 

most up-to-date limits and conditions to protect human health and aquatic life, 

thereby delaying needed improvements in water quality. EPA’s position is that 

permit renewals can impact water quality in a number of ways such as through 

more stringent technology-based limits for existing permits, limits on new 

parameters, water quality-based limits, whole effluent toxicity limits, best 

management practices, and improved monitoring requirements. This analysis is 

limited to nationally available data for numeric limits. While as discussed above, 

backlogged permits do not appear to be a significant cause of impaired waters, 

analysis of final numeric limit changes and limited examination of related 

discharges further supports EPA’s new direction in prioritizing permits for 

reissuance according to potential environmental significance. Finally, building on 

this type of analysis would also help develop a detailed understanding of the 

sources of these limit changes (such as water quality standards, effluent 

guidelines, and TMDLs) that would assist in managing the Clean Water 

programs. 

While a large majority of the backlogged major permits reviewed (2,166 of the 

2,681, or 81 percent) had at least one limit change,3 the majority of pre-existing 

controls on pollutants did not appear to change (about one-third of the continuing 

controls on discharges showed changes). However, about half of the permits also 

contained controls for new parameters. (See Appendix C.) Out of the 5,555 

major permits recorded as current in June 2003, we analyzed about half (2,681 

which appeared to have been delayed over 45 days and had a prior permit with 

matching limit data). For a national review, analysis was limited to the data 

available in a national data system (limits), and conclusions are also limited and 

qualified by overall PCS data concerns. (See Appendix A for methodology in 

selection and screening of permit data and permit limit records). By comparing 

prior backlogged and current permit limits, we identified changes including 

increasing, decreasing, and additional limits for previously controlled pollutants 

as well as for newly limited pollutants. Any identified change in a permit could 

be viewed as significant and, therefore, this analysis supports the continued 

3

 Limit increase, decrease, new additional limit for a previously controlled pollutant, or limit for a new 

parameter. Deletions of limits were not counted as a change. 

20 
timely reissuance of permits. In the analysis of numeric limits, the addition of 

limits for the first time for new parameters could also be of greater environmental 

significance than some of the other changes noted, but we were unable to quantify 

this impact for permit delays; the parameter may have been discharged and 

monitored or may only have been permitted to discharge at the time of the permit 

renewal. Our next step focused on limits identified as becoming more stringent 

due to concerns that these would have represented delayed environmental 

benefits, and to examine whether permit limit changes were representative of 

delayed environmental impacts, including benefits. 

Even where PCS data show that permit limits are becoming more stringent, the 

impact of the permitting delays varies and not all cases may have resulted in 

environmental degradation. Analysis of a small subset of reviewed data, about 

200 permits and approximately 1,000 total final quantity maximum and average 

limits4

 which became more stringent, showed that most related discharges were 

already in compliance with the revised limit. This data represents a subset of the 

permits identified with decreased limits overall and for quantity limits due to data 

constraints, so conclusions are not generalized. Facility discharges while under 

the prior (backlogged) permit were in compliance with the revised limits for the 

majority reviewed. The data illustrates both that limit changes upon reissuance of 

a backlogged permit is not only variable but also that it may not equate to 

environmental degradation due to delayed permit issuance (see Table 3.1 below). 

Table 3.1: Discharge Monitoring Report Data From Prior Permits Compared to 

Quantitative Limit Decreases in Revised Permits 

Backlogged 

Permits 

Quantitative 

Maximum Limit 

Decreases 

Quantitative 

Average 

Decreases 

Discharge Monitoring Report data 

available from prior permit coverage 

period5 

265 710 503 

Discharge Monitoring Report data 

reported under prior permit comply 

with revised current limit 

196 579 404 

Discharge Monitoring Report data 

reported under prior permit violate 

revised current limit at least once 

68 (maximum) 

54 (average) 

131 99 

Of violations identified, all violations of 

current limit also violated prior limit 

25 (maximum) 

16 (average) 

50 24 

4

 This subset may not include all PCS data for decreased quantitative maximum and average limits as 

various types of parameters were excluded from the analysis such as flow, temperature, dissolved oxygen, and pH. 

The data are shown for illustrative purposes only and should not be generalized. 

5

 These permits and limits are a subset of those identified with at least one limit decrease and of the set of 

changes identified for quantitative limits due to data constraints. 

21 
This analysis also supports prioritization of permit reissuance due to various 

indicator factors. Where discharges were above the revised permit limit, the

delay in permit reissuance may be more environmentally significant. However,

where the facilities’ discharges were also not in compliance with the prior limits,

backlog status of the permit may not be the sole factor in possible delays in

environmental benefits or improvements seen from permitting activities. These

might be impacted by compliance and enforcement or other issues. We did not

attempt to determine why facilities met new permit conditions beforehand. 

However, explanations include that the facility adjusted to an upcoming change

prior to permit receipt, or that the change was not significant. (See Appendix A

for methodology for Discharge Monitoring Report comparison.) 

Overall, the results of our analysis support the prioritization of permit 

reissuance according to factors indicating potential environmental significance. 

Our analysis indicates that environmental significance of reissuance of previously

backlogged permits is variable. 

Environmental Significance of Backlog Could Increase in Future 

EPA is making changes that will affect a number of clean water programs that 

support NPDES permitting and which, in all likelihood, will increase the NPDES 

program’s importance. Consequently, this may increase the importance of the 

backlog in the future. Further, EPA’s encouraging identification and 

prioritization of permitting resources for permits likely to need changes will affect 

the environment. 

In the future, more permit limits may change on reissuance based on planned 

activities in supporting programs. Permit limit changes are driven by regulatory, 

facility, or environmental factors, many of which EPA has identified in a national 

review checklist (see Appendix D for additional factors identified). To better 

describe the future potential for environmental significance in the backlog, we 

reviewed information for three national programs for which we expected planning 

information or data to be available at the national level (water quality standards, 

TMDLs, and effluent guidelines) as well as two recent national initiatives 

(watershed permitting and pollutant trading). Although national data were not 

readily available to analyze individual permits, overall, we expect these programs 

to increase the value of permit reissuance. Currently, States may be better 

positioned than EPA to identify priority permits in the backlog for permit 

reissuance based on likely permit limit changes. Details follow. 

Water Quality Standards. New and revised water quality standards should 

increase the environmental significance of backlogged permits, since they are one 

of the bases for deriving permit limits. While we could not determine the current 

effect of delayed water quality standards on the backlog due to the backlog of 

water quality standards or delayed triennial reviews, information on overall 

program management indicates there will be changes in water quality standards 

that are likely to affect permits. In 2000, EPA reported water quality standards 

22 
submissions had been steadily increasing since 1996. Additionally, EPA also 

recently issued revised and new human health criteria, which is likely to lead to 

more permits in the backlog changing due to new or revised water quality 

standards. 

EPA’s 2003-2008 Strategic Plan reflects EPA’s commitment to ensuring effective 

operation and administration of the standards program, including triennial review 

and revision as required by the Clean Water Act. In the 2005 national program 

guidance, EPA notes that it is working to increase the number of States and 

authorized Tribes performing triennial reviews. EPA’s planned activities also 

indicate the potential for more water quality standards changes. According to the 

FY 2005 Congressional Justification, EPA will be focusing on reducing the 

backlog of water quality standards, establishing highest attainable uses, and 

strengthening the scientific foundation. The 2005 national guidance also states 

EPA expects to develop criteria documents for 15 pollutants by 2008, as well as 

develop nutrient criteria, adopt biological criteria, and provide assistance for 

adoption of water quality standards. Also, there are a number of emerging 

contaminants and issues that will need to be addressed. 

Total Maximum Daily Loads. More EPA-approved TMDLs addressing impaired 

waters are expected in the future, which will increase the environmental 

significance of permit reissuance through incorporation of WLAs to address point 

source contributions to impaired waters. While it is possible that pre-TMDL 

water quality-related data may be incorporated into a permit or WLAs will result 

in the same limit as conventional calculations, completion of future EPAapproved TMDLs is likely to be related to more permit changes. Waters not 

meeting water quality standards are reviewed for inclusion on the impaired waters 

list requiring a TMDL to address the impairment. About 9,738 TMDLs were 

approved from 1996 through early 2004 and, currently, about 40,000 TMDLs will 

need to be completed (although not all of these will be associated with point 

sources). There are various reasons to expect an increase in the number of 

TMDLs that may be associated with NPDES permits. New and revised water 

quality standards could drive new and revised impaired waters assessment. Also, 

only one-third of waters have been assessed for whether they meet designated 

uses, and while EPA expects the remainder to have a lower rate of impairment, 

more impairments may nonetheless be identified. 

Effluent Guidelines. Because EPA is reducing resources to the effluent 

guidelines program, we believe that over time this program could have a 

diminished impact on the environmental significance of backlogged permits and 

as of reissuance of permits in the program as a whole. The effluent guidelines 

program is the technology-based component of the clean water program; EPA 

identifies the pollution reduction capabilities of industries, and develops national 

requirements that permit writers use when writing permits. Effluent guidelines 

contribute a limit change where they are new or revised since an industrial permit 

in a covered sector was last reissued (where the technology limit is more stringent 

than the standards based one); the majority of effluent guidelines were 

23 
promulgated in the 1970s and 1980s and, although subsequently reviewed, few 

have had subparts updated according to the draft effluent guidelines strategy 

published in November 2002. EPA’s Strategic Plan for 2003-2008 states that 

regulations are now in place for most major industrial classes. 

EPA recently dramatically reduced the resources to the effluent guidelines 

program, and, according to EPA’s plans, few major facilities in the June 2003 

NPDES backlog are anticipated to be affected by effluent guidelines in the near 

term. We believe that this could result in a decline in the environmental 

significance of backlogged permits. Although the impact of this program in all 

likelihood will decline in the future, permits currently in the backlog will continue 

to be affected by changes in the guidelines. Several guidelines were written in the 

last decade and there are plans to develop new guidelines, although possibly at a 

slower rate. 

Watershed Permitting and Pollutant Trading. There are several innovative 

approaches within Clean Water Act programs that can increase the sources of 

limit changes and, therefore, the likelihood of changes needed in reissued permits. 

Consequently, any affected permits that are backlogged will also have a higher 

environmental significance. Watershed permitting and pollutant trading can 

provide alternative means for developing permit limits: 

• EPA is promoting use of a watershed approach designed to develop NPDES 

permits for multiple point sources located within a defined geographic area 

(e.g., watershed-based individual permit, watershed general permit, integrated 

municipal permits). 

• EPA’s recent pollutant trading policy allows facilities to meet regulatory 

obligations by purchasing environmentally equivalent pollution reduction 

from other sources if consistent with water quality standards. 

Using new approaches like watershed permits or trading may result in changes to 

permits for NPDES permitted facilities. If there are delays in reissuing affected 

permits and in incorporating any resulting new limits, this may result in delay in 

seeing benefits from these programs. Further considerations for these two 

programs relate to categorizing the environmental significance of permits and 

managing interactions between program elements. Major permits may receive 

permitting priority over minors because of their designation as a major and rather 

than because of relative environmental importance of permit reissuance. EPA 

supports issuance of permits within a watershed management framework, such as 

a rotating basin approach, in which point source permitting decisions should be 

made based on environmental priorities outlined in basin management plans. As 

part of this effort, EPA established a flexible policy allowing for a backlog where 

permitting authorities demonstrate progress toward implementing a watershed 

permitting approach. Also, pollutant trades between two facilities not being 

addressed in a particular permitting cycle may require a permitting authority to 

address permits not expected in that year’s annual workload, while needing to 

24 
address major permits can require permitting outside of a planned 5-year rotating 

basin permitting cycle. 

EPA Should Continue Promoting Prioritization of Permit Issuance 

EPA is developing and implementing various overall strategies to more efficiently 

reissue permits and, thus, ultimately reduce the potential universe of the backlog 

(see Chapter 2). Fewer permits in the backlog, expired for less time, would assist 

in reducing the potential significance of the backlog simply in terms of numbers 

and age of permits. However, if 100-percent permit coverage cannot be achieved 

and maintained while ensuring high quality permits, it is important for EPA to 

prioritize this work to achieve the greatest environmental benefits possible. 

The continuance of current permit and priority issuance targets through 2008 

shows that EPA recognizes that addressing backlogged permits is likely to remain 

a challenge into the future. Therefore, it is moving State and regional permit 

writers to focus attention on that part of the backlog that is most likely to be a 

problem for water quality. The principal way it is doing this is having States and 

regions identify “priority permits” and work toward the goal of maintaining 

95 percent of them as current. However, EPA regional and Headquarters officials 

recognize that the number of backlogged permits could increase in response to 

this 95-percent goal, which would require resolution of potentially more complex 

issues and therefore take longer to reissue these permits. 

Other considerations sometimes conflict with EPA’s encouragement of States and 

regions to emphasize permit writing for those facilities where a reissued permit 

would most benefit water quality. For example, modification of an existing, 

current permit may be as or more environmentally significant than reissuing a 

backlogged permit. In addition, some States prioritize issuance of new permits 

over reissuance of existing permits, in part because these facilities could not 

legally begin discharging without the issuance of a final NPDES permit. While 

the backlog ostensibly accounts for these new permits, several States and regions 

contacted stated that new permit applications are not recorded in PCS until a final 

permit is issued (see Chapter 4). 

Data gaps and errors currently hamper EPA’s ability to prioritize permits based 

on desired characteristics. There are known data gaps in PCS, especially for 

minors. Other national databases are incomplete or difficult to incorporate into 

permitting decision making. The NPDES Permitting Division developed two 

web-based characterization tools to help pre-screen potentially environmentally 

significant permits using national information, but they are currently impacted by 

data limitations. EPA has asked States to develop the priority permits lists for 

backlog reissuance with regional input, but EPA will need to develop appropriate 

oversight tools to manage this effort. 

* * * 

25 
Conclusions and recommendations for this chapter are presented in Chapter 5, 

where they are integrated with conclusions and recommendations from other 

chapters. 

Agency Comment and OIG Evaluation 

In its response to the draft report, EPA acknowledged that permits in and of 

themselves do not protect water quality, but are a key element in the structure and 

the Agency's implementation of the Clean Water Act. Overall, EPA agreed that 

addressing the backlog alone may not provide an effective strategy to improve 

water quality; the NPDES program is one part of the implementation of the Clean 

Water Act architecture. 

EPA did not agree that the backlog reduction has had a limited impact on water 

quality. EPA indicated that to reach this conclusion, the report relies on an 

analysis of Discharge Monitoring Report results on existing limits from a small 

subset (12 percent of the sample) of reissued permits. EPA commented that this 

discussion should be augmented to reflect the variety of ways in which permit 

renewal has an effect on water quality (for example, more stringent 

technology-based limits for existing permits, limits on new parameters, water 

quality-based limits, whole effluent toxicity limits, best management practices, 

improved monitoring requirements). EPA further stated that the analysis omits 

very important parts of the permit program universe, such as control of 

stormwater and indirect discharges through the pretreatment program. EPA stated 

that this analysis focused on the effects of the backlog and therefore did not 

address the NPDES program outside of the backlog definition. 

The most significant source of impairments of waters is acknowledged by EPA to 

be nonpoint source pollution. Our analysis also indicated the backlog of permits 

played a limited role as a source of impairment. Further, our review focused on 

the backlog and backlogged permit limits by design, and we therefore added 

descriptions of NPDES program areas that were outside of the scope of the 

project overall to address EPA’s comments regarding scope of the review. We 

agree with EPA that there are other components of permits that were not 

addressed by our analysis of final numeric limits in previously backlogged 

permits that had been reissued. However, the analysis of permit changes was 

limited to where data was available in a national database and the scope of the 

analysis was clarified in the text. The records originally reported in the draft as 

not analyzed because of changes in unit codes were analyzed using a standard 

unit code data column from PCS, and this information was added to the analysis. 

This caused changes in numbers reported in the draft. We reframed the 

discussion of the analysis of the limits and of the associated Discharge 

Monitoring Report analysis to reflect the limited nature of this study. While the 

results may not be generalized, they illustrate examples where permit limits may 

not have substantially changed as well as examples of limit changes not 

necessarily having contributed to environmental degradation as discharge changes 

may not have been required. Therefore, we draw the same conclusions that EPA 

26 
should prioritize reissuance of permits within resource constraints to maximize 

environmental improvements. We also clarified points throughout the chapter as 

well as addressed any technical issues raised by EPA, as appropriate. 

Several comments referred to the effluent guidelines program. Overall, EPA 

believed that the report should give greater recognition to the impact that 

implementation of effluent guidelines promulgated in the last decade or more will 

have on water quality as it continues to implement the NPDES program. EPA 

stated that permits last updated 6, 8, or 10 years ago will not reflect the improved 

technology-based limits that are contained in the guidelines promulgated during 

the 1990s and earlier in this decade. Two prominent examples of guidelines that 

are expected to have a substantial impact are the 316(b) rule and the CAFO 

regulations. EPA stated that all the effluent guidelines promulgated in the last 15 

years would still be relevant today for any permits that expired before a new 

effluent guideline was issued. EPA also stated that permits in the backlog are of 

varying ages. These reasons describe why EPA considers it a priority. 

EPA further commented that the issue of guidelines is significantly downplayed 

because the number of guidelines being revised or developed related to point 

sources is very small. EPA stated that this can be misleading because some of the 

recent guidelines have potential for significant impact (for example powerplant 

intake structures, CAFOs, centralized waste treatment, etc.). If a permit has been 

backlogged for a significant number of years, these new guidelines may not yet be 

reflected in the permit. EPA also indicated that it should be mentioned that 

effluent guidelines are one of the factors EPA is using for priority permits. 

We agree with EPA that inclusion of new or revised effluent guidelines in permits 

may result in significant changes in permits, as described in a prior OIG report 

(see Appendix A). However, this project focuses on impacts of delayed 

reissuance of permit limits in backlogged permits. As EPA points out, some 

facilities adjust to expected effluent guidelines even before a permit is revised, 

reducing the significance on environmental impacts of delayed permit reissuance. 

Also, while inclusion of effluent guidelines in a revised permit may be significant, 

the impact of the program depends on how many of the backlogged permits have 

an associated new or revised effluent guideline to be incorporated. Therefore, we 

have revised the discussion to reflect potential significance of effluent guidelines 

where incorporated but still conclude that the number of new or revised effluent 

guidelines that will affect discharges of facilities with backlogged permits in the 

future will nonetheless determine the overall impact on the backlog. 

27 
Chapter 4

Backlog Reporting Has Provided 

Inadequate Measure of Environmental Results 

EPA’s Government Performance and Results Act (GPRA) backlog measure 

reporting did not provide an accurate view of the status of the NPDES permit 

program or an adequate measure of environmental results. These measures were 

not useful for making management decisions because: 

• Measures incorporated data reflecting backlog definition changes and data 

corrections that were not accounted for in baselines. 

• The measures generally were of outputs that did not necessarily reflect 

outcomes (environmental impact) of implemented management strategies. 

The baseline and measure for the backlog have been completely revised to be 

consistent for FY 2005. Until that time, the failure to replace the baseline resulted 

in an inappropriate baseline being compared against measures. This includes the 

effects of program management or changes (e.g., inactivations and changes to 

general permitting) in the permit universe and backlog accounting. GPRA makes 

agencies accountable to Congress and the public on their performance by 

requiring reporting on goals, resource needs, and results. Other EPA GPRA 

measures relying on permit data are also impacted. EPA has recognized 

weaknesses and begun improving program oversight and modernizing the PCS 

database. 

Improvements in Backlog Measurement Affected Reported Progress 

In the FY 2005 National Program Guidance, EPA published a new combined 

measure for backlogged permits with a baseline from October 2002 that reflects 

increased accuracy and improved program measurement. An additional measure 

developed in conjunction with PER has also now begun tracking backlogged 

permits prioritized for reissuance. However, due to the refinements needed to 

improve the measure and program oversight, prior GPRA backlog reports 

showing improvements were impacted by measure changes, data corrections, and 

an inconsistent baseline. Overall improvements in the measure included both data 

cleanup as well as modifications in tracking to better reflect the program. As a 

result, EPA (1) changed the backlog definition, which contributed to 

improvements in the reported measure; (2) oversaw the data cleanup of thousands 

of inactive facilities in PCS that inflated the 1998 backlog measure and the 

permitting universe; and (3) corrected other data errors identified. 

Although EPA explained the backlog definition changes in the data verification 

and validation section of annual plans and reports, EPA did not accordingly revise 

the GPRA baseline until 2005 to reflect the measure revised in 2002. Therefore, 

28 
the historic tables showing multiple years’ reporting appear comparable when 

they need to be interpreted in the context of the then-ongoing changes. 

Difficulties interpreting the data may be compounded because they are 

represented as comparable across years; the FY 2004 Annual Plan Verification 

and Validation of Performance Measures states: “The data are suitable for yearto-year comparisons of officially tracked permit status.” 

Table 4.1 shows the actual results for percentage of currently permitted facilities 

as reported annually for GPRA. The GPRA reporting format for FY 2005 

changed in the Annual Plan and Congressional Justification, but according to an 

EPA memo and National Program Guidance, the backlog is still being tracked. 

However, the new backlog goal reflects a combined permit measure and baseline 

from 2002. 

Table 4.1: Percentage of “Current” Permits (Not Backlogged) Reported Through 

GPRA as Compared to Original Backlog and GPRA Baseline

Permit 

Type 

Original 

Backlog 

in Nov. 

1998 

GPRA 

Baseline 

May 

1999** 

FY 

1999 

FY 

2000 

FY 

2001 

FY 

2002 

FY 

2003 

FY 

2004 

Major 74% 73% 71% 72% 75% 83% 84% 86% 

Minor* 52% 54% 62% 70% 75% 74% 84% 87% 

* Definition of which permits are counted in the minor category has changed over time. 

** May 1999 GPRA baseline shown in GPRA reports, including the FY 2004 Annual Plan. 

However, the Annual Report for FY 2004 does not show a baseline. 

The OIG and EPA identified the backlog as a significant management problem in 

FY 1998. EPA identified the backlog as a corrected material weakness in 

FY 2002. In the 2002 Integrity Act report, the Agency stated that, in November 

1998, 26 percent of majors and 48 percent of minors did not have current permits. 

By the end of FY 2002 the Agency downgraded the Federal Managers’ Financial 

Integrity Act status of the backlog based in part on the percentage of improvement 

reported, as indicated in the Integrity Act section of the FY 2002 Annual Report: 

Since the Agency identified this weakness in 1998, it has achieved 

56 percent of targeted reduction in the backlog of major point 

source permits and achieved 58 percent of targeted reduction in 

the backlog for minor point source permits. EPA’s comprehensive 

strategy for improving the NPDES permit program has resulted in 

noteworthy progress, and it establishes a management control 

framework for continued improvement. 

Backlog improvements have resulted from administrative changes (e.g., data 

cleanup, changes to the backlog definition) and continued permit issuance. The 

cleanup of databases improved the accuracy of the universe of permits and 

modifications to the backlog definition better reflect current permitting 

approaches – however, these are important considerations when evaluating 

29 
backlog improvements reported. The altered approaches, practices, and tools 

designed for permit issuance identified in Chapter 2 were beneficial, but did not 

explain all of the improvement in the backlog reported by EPA in 2003. Changes 

in the permit backlog universe reflect a more accurate accounting of the number 

of active permits but also change the denominator, so that the changes in the 

percentage of current permits over time may reflect more than simply changes in 

rates of permit issuance. For example, from November 1998 to June 2003 (and 

updating to March 2004): 

• by March 2004, there were almost 600 more current majors but about 100 

fewer permits in the majors universe; 

• there were about 2,300 more current minors reported in June 2003, but by 

March 2004 there were only about 450 more current individual minors than in 

1998, while the individual minors universe decreased by about 22,500; and 

• there were about 3,600 fewer current facilities covered by general permits in 

2003 than in October 2000, and only about 2,600 fewer current facilities 

reported in March 2004, but the general permitted minor universe also 

decreased by about 10,000 by March 2004. 

Details are in Appendix E. 

Significant Portion of Reported Improvement Due to 

Definition Changes 

EPA has incorporated a number of changes (see box on next page) since the 

original backlog reporting in the measure and baseline established beginning in 

FY 2005 (to be used through 2008). EPA reported these changes in the data 

verification sections of the Annual Plans and Reports to develop a more accurate 

universe and measure. While these changes result in overall improvements to the 

measure, the results of these changes also include additional backlog 

improvements from an administrative change extending the time allowed after 

permit expiration before including a permit in the backlog. 

Prior to January 2002, any permit expired more than 45 days was included in the 

backlog (allowing for data entry according to PCS data entry arrangements 

between States and Regions). EPA states that a focus on permits languishing in 

the backlog rather than those delayed weeks or months due to administrative 

hurdles prompted a backlog definition change. In January 2002, EPA redefined 

the backlog to include permits only 180 days after permit expiration. According 

to the Agency, the additional time was needed to allow for delays in PCS data 

entry; allowance for incomplete applications; draft permits requiring revisions 

from public comments, and other reasons extending the permit issuance process. 

At the time of this change, EPA reports it was already beginning to steer toward 

identifying high and low priority permits, recognizing that while inventories of 

30 
the backlog were important, they may not necessarily correlate with 

environmental improvements. A priority permit approach (and measure) is now 

in place as part of PER 

(discussed below). While this 

change may more accurately Changes to Backlog Definition: 1998-2004 

reflect EPA’s focus, it also 1. From November 1998 through December 2001, 

contributed to an additional the backlog percentage was based on dividing all 

individual permits (non-Stormwater), individual major improvement in the backlog stormwater permits, and general (non-Stormwater) status in June 2003 by major permits expired 45 days or longer, plus the 

increasing reported current total number of permits with no issuance data and/or 

perm no expiration date, by the total number of active it coverage 3 percent for permits as defined. individual minors and 

2. As of January 2002, permits were considered 3.6 percent for majors. backlogged if expired 6 months or greater. 

3. Beginning with the September 2002 backlog In March 2004, EPA also reports, individual permits issued by EPA in 

authorized States were no longer reported as State 

permits but separately as EPA permits. 

extended the length of time 

allowed before a permit 

application is considered 4. Beginning with the early Spring 2003 backlog 

reports, the backlog percentage was changed to backlogged from immediately reflect the current percentage rather than backlog 

to over 1 year. EPA is percentage. 

considering further modifying 5. Beginning with October 2002 backlog reports, 

minor facilities covered by non-Stormwater general 

permits listed in ePIFT were included in the definition 

the definition to differentiate 

permit applications received of the backlog. without complete information 

6. In March 2004, applications were counted after (see external causes of the 1 year as backlogged. 

backlog discussion in Chapter 7. EPA is proposing backlog credits for incomplete 2). However, it is difficult to applications and delays due to initial implementation 

determine the impact of this 

change on the backlog because 

several of the States and 

regions contacted indicated they have ceased recording applications in PCS. 

Thus, new permit applications were not always entered until a final permit was 

issued; while technically not an environmental impact since a point source legally 

cannot discharge without a permit, new permits may be important due to 

economic impacts. While providing the State with more control over the 

permitting process, if applications are not entered into PCS until a permit is final, 

the measure undercounts the workload the permitting authorities are processing. 

Although we are unable to precisely estimate the impact of the changes to the 

application backlog criteria, available PCS data for original permit issue date 

indicates approximately 125 majors and about 4,380 minors in the active universe 

of permits have been originally issued since November 1998, although there were 

many permits that did not have this data for analysis. 

EPA has taken a series of steps revising and improving the backlog measure and 

data, which have been incorporated into a new FY 2005 measure and 

accompanying 2002 baseline. In one significant change, EPA amended the 

31 
backlog definition to include general non-stormwater minor permits once 

consensus was reached with permitting authorities on the backlog inventory and 

to more accurately describe permitting of facilities as regions and States started 

using more general permits. In October 2002, this change increased the universe 

of minor facilities in the backlog reports by 64,825, of which only 8,124 were 

actually backlogged. While the resulting measure more accurately reflected the 

permitting universe, it also increased the apparent improvement in the minors 

backlog in 2002 because EPA started reporting on the backlog status of general 

permitted minor facilities but did not adjust the goal description or original 

baseline for the measure. 

While not in the reporting tables, the information on the definition change was 

noted in the Data Verification Section of the reports. The FY 2003 Annual 

Report stated the goal for issuing minor permits was met while there was a 

continuing challenge in meeting the majors goal due to competing priorities and 

increasing complexity of permits in a watershed context. Although EPA 

identified these as the same goals with different targets, in actuality the goal and 

target for majors stayed the same while the goal and target for minors both 

essentially changed from FY 2002 to 2003. 

However, the inclusion of generally permitted minor facilities was not clearly 

stated and the associated level of achievement was higher than would have been 

reported. While backlog tracking practices make it impractical to go back in time 

to adjust the 1999 baseline, EPA could have clarified that the reported values for 

the years preceding FY 2003 were not comparable to the new measure (see Tables 

4.1 and 4.2). EPA also could have established a new GPRA baseline including 

the correct universe of permits from which to measure progress as was done 

within the Office of Wastewater Management or as shown in the backlog status 

reports. In the FY 2005 National Water Program Guidance, EPA has resolved 

this issue by combining the entire measure (including for major and minor 

permits) and using a combined 2002 baseline. 

32 
Table 4.2: Different Backlog Goal Baselines for GPRA and Office of Wastewater

Management

GPRA Baseline 

(May 1999) for 

Current Permit 

Coverage 

Office of Wastewater 

Management Baseline 

for Current Permit 

Coverage (in 2000) 

Baseline Shown 

in Backlog 

Status Reports 

(in 2003) 

Majors 72% 72.1% (January 2000) 

Individual Minors 54% * 66.7% (August 2000) 

Minors 

(with non-stormwater 

General permits) 

N/A * 88.2% (October 2000) 

Minors: Combined 

Individual Minors 

with non-stormwater 

General permits 

N/A* N/A 

N/A 

66.7% 

(August 2000) 

N/A 

80.8% 

(October 2000) 

* Individual minor permits used for the baseline in GPRA for “minors.” 

Properly Identifying Inactive Permits Removed Significant Number 

from Backlog 

Because inaccurate PCS data exaggerated the number of permits in the backlog 

for active dischargers, recent PCS data cleanup accounted for removal of 

significant numbers of permits previously counted in the backlog. The PCS data 

cleanup was necessary, but the backlog baselines should have been replaced with 

comparable data so that changes in the measure reflect programmatic 

improvements and not PCS data cleanup. 

EPA defined the backlog to include only those applications and individual 

permits that are active dischargers (facility inactive code “A” in PCS). However, 

over time, permitted facilities discontinue discharging, or permit applications are 

withdrawn without a corresponding change to their PCS status. Inactive facilities 

and applications erroneously still coded as active inflated the November 1998 

backlog for minors by almost 40 percent based on inactivations through April 

2004 (see Table 4.3). We did not consider permits removed from the backlog due 

to inactivations to have environmental impacts. 

33 
Table 4.3: Inactivation of Permits Backlogged in November 1998 

(November 30, 1998 - April 9, 2004) 

Number of permits in 

Permits from November 1998 

backlog that were inactivated * 

Permit 

Type 

November 1998 

reported backlog I G Total 

Majors 

Individual Minors 

1,791 

30,988 

61 

12,054 

2 

276 

63 

12,330

 I = Inactive (Permits for inactive facilities no longer discharging). 

G = General (Permits covered under general permit instead of individual).

 * = For facilities with both expiration and inactivation date data in PCS. 

Also, as current permits are being inactivated, States and EPA have had to issue 

permits for facilities in the backlog, issuing new permits, as well as renewing 

expiring permits at a rate high enough to still maintain and improve current 

permit percentage levels. The impact of inactivations is difficult to quantify, 

since some “current” permits are inactivated shortly before expiration or being 

given backlog status while others are inactivated earlier. Although the backlog 

measure may be appropriate for some management purposes, permit issuance 

statistics should also be used to track State program management that could 

otherwise be obscured by necessary PCS permit universe data management. EPA 

recognizes that permitting authorities have improved permit issuance in the face 

of declining resources, additional programs coming online, and other competing 

interests. As these may not be well reflected by the backlog measure (e.g., most 

stormwater permits are not included in the backlog accounting inventory), permit 

issuance and other measures included in the Management Report might be 

considered to reflect this. 

EPA continues to support cleanup of PCS data. EPA has supported inactivation 

of non-discharging permits and assisted with the data cleanup through contractor 

support. EPA believes that there are still some permanently inactive facilities that 

have not been updated in PCS but that this is a program management issue that 

needs to be addressed by the permitting authorities. EPA is still providing 

resources to support States in completing links to PCS from State databases as 

well as cleaning up existing data. States have been trying to complete data links 

to PCS to be able to upload up-to-date information to EPA’s system instead of 

having to perform double data entry. EPA’s continued assistance appears 

beneficial, since 7 of 10 EPA regions and 4 of 8 States in our survey group 

indicated a desire for EPA assistance for PCS data cleanup. 

EPA believes that raising awareness of the implication of “bad inventories” will 

prevent the reoccurrence of the 1998 situation when it was impossible to obtain 

reliable inventories. Initially, PCS indicated that there were about 71,000 

facilities with individual permits and there was no way of knowing which 

facilities were inactive (they appeared as legitimate facilities). This was 

complicated also by anomalies in PCS where inactivated facilities are only 

34 
temporarily in non-discharge status. EPA states that the Integrated Compliance 

Information System (ICIS) will allow for linkages to be drawn to improve 

reporting abilities. EPA also provided an example of a PCS data entry agreement 

with one State that includes cooperating to update and maintain permit tracking 

for active facilities and inactivating facilities that no longer discharge. 

Other Data Errors Undermine Backlog Measure 

Backlog accounting is also affected by other data errors (such as PCS expiration, 

or issuance and effective dates missing, out of sequence or in the future). Also, 

lack of ePIFT guidance has resulted in a lack of uniformity in reporting generally 

permitted facilities as backlogged. Missing information, particularly, for minors, 

is a known PCS problem that will hamper environmental characterization (see 

Chapter 3). Further, although not impacting the backlog measure because the 

permit expiration date was updated, we identified 930 permits to be removed from 

the analysis of permit changes; these current permits appear to still have the prior 

permits’ limits listed in PCS. This is an issue recognized by the Office of 

Enforcement and Compliance Assurance, and this issue limited our ability to 

analyze permit changes as reported in Chapter 3. 

Oversight Improvements Prompted Changes in Reported Backlog 

EPA Headquarters and regions, as well as States, have undertaken a number of 

oversight activities, including recent State profile data collection, resulting in 

improved information leading to necessary adjustments of backlog data. For 

example, EPA has identified non-standard usage of PCS requiring adjustments to 

backlog data in two States and a region. In one instance, EPA removed what had 

appeared to be about 20,000 generally permitted “facilities” from the backlog 

accounting universe in Region 6 where pipes were being counted instead of 

facilities. Also, recently EPA needed to adjust data for Minnesota and New 

Jersey because of non-standard use of PCS. Additionally, because “A” type 

permits are not currently included as a source of backlog data, the measure may 

be over- or underestimating CAFO permits. 

Backlog Measure Still Does Not Capture Some State Management 

Approaches 

Two overall State management approaches are also not well-represented by the 

backlog accounting: 

• In Michigan, all permits expiring in a given year expire on the same date at the 

beginning of the fiscal year, resulting in a cyclical backlog pattern. Michigan 

finds this management approach beneficial because it allows them to address 

multiple, related permits as needed within a rotating basin approach. 

However, 180 days after the expiration date, the backlog measure shows the 

remainder of permits scheduled to be addressed in the year are reissued as 

35 
backlogged, which then is reduced over the course of the next 6 months. Due 

to adoption of a different permit management approach, the backlog measure 

(including 180-day delay from expiration date) does not reflect Michigan’s 

management approach well. 

• New York implemented a system of administrative renewals of expiring 

permits which lessened the usefulness of the backlog measure. Upon receiving 

“short form” renewal applications, the State administratively renewed permits, 

updating the issuance and expiration dates without a corresponding technical 

review of a full permit application. Permits requiring changes were identified 

as prioritized permits and any substantive changes to these permits were made 

by modifications following a technical review. EPA did not consider the 

administratively renewed permit to be backlogged because the expiration date 

in PCS is “current” - even though these permits are substantively no different 

than an expired or backlogged permit in another State. After almost 10 years, 

EPA Region 2 and New York recently agreed on steps to revise the State’s 

permitting process to comply with Federal requirements (see Chapter 5 

recommendations and discussion of comments for further details). While 

administrative renewal will no longer be allowed for four specified permit 

types (e.g., permits needing a new limit consistent with a wasteload allocation 

in an EPA-approved TMDL, etc.), the backlog status for these will not be 

affected until the current permit expires, sometimes years in the future. The 

deadline is October 2006 for full implementation of the program changes in 

New York. Although we cannot precisely quantify the impact this practice has 

had on the backlog measure, it doubtless contributed to EPA’s overstating the 

improvement. However, the impact was not insignificant because, in June 

2003, approximately 6 percent of the current major permits nationwide were in 

New York. In June 2003, the backlog status report indicated that 344 of 354 

(97 percent) of New York’s major permits were current. 

Backlog Measure Has Not Reflected Environmental Outcomes 

In addition to inconsistent permitting strategies and inconsistent data, the 

usefulness of the backlog measure has been undermined because it is not closely 

tied to the environmental outcomes discussed in Chapter 3. Although simply 

having a current permit has value, the backlog measure is an output measure that 

should be more closely tied to the program’s environmental outcome goals of 

reducing loadings and improving water quality. The backlog measure fails to 

reflect that, even assuming current or backlogged permits have a consistent 

meaning, they in and of themselves do not reflect environmental improvement. 

The 90-percent current permit target of the backlog goal does not have a clear 

relationship to environmental impact in terms of loadings or water quality. 

EPA has developed a new measure for priority permits under its PER Strategy 

based, to some degree, on environmental characteristics. However, in the 

meantime, the backlog measure has been and is being used in management 

36 
decisions. Therefore, the backlog measure may be driving some inefficient 

decisions. Further, the GPRA measures designed to reflect environmental 

outcomes from the NPDES program (and supporting programs) are flawed due to 

many of the same issues affecting the backlog measure. 

Inconsistencies Make Backlog Measure Unclear 

Current reissued permits are not equal in terms of environmental impacts. 

Permits are not comparable output units in terms of environmental impact or 

even issuance resource requirements. Determination of environmental 

significance is complicated for a number of reasons. A State’s permit may 

govern discharges of pollutants that are of concern in a downstream or adjoining 

State, or water quality impacts of some minor permits could be more significant 

than some majors, depending on discharge clusters and other factors. Water 

quality of waters receiving point source discharges is not determined by whether 

discharges are regulated by current permits; rather, it is determined by water 

quality monitoring and assessment. 

EPA stated in response to the draft report that it views the backlog measure as 

capturing program integrity rather than environmental significance. However,

the backlog measure has not provided the management information that EPA

intended as described in the 2004 Annual Performance Plan and Congressional

Justification. EPA had stated that “Together the PCS and (e)EPIFT data are

intended to measure NPDES program coverage of facilities with up-to-date

permit requirements.” The backlog measure assumes an equality between

“current” permits and up-to-date limits. However, permits defined as “current”

by the backlog measure are not necessarily consistent in containing up-to-date

limits. Inconsistent meanings of the term “current permit” undermine the

reported measure. For example: 

• Modifications: Some current permits need modifications to reflect new 

information or changes in environmental or facility status. PCS modification 

data showed that approximately 2,000 of the 5,500 current major permits as of 

June 2003 had modifications based on PCS data showing records with 

between 1 and 7 modifications. 

• Expired permits: Some apparently current permits were actually expired (up 

to 180 days) and therefore may have limits no longer up to date. For the June 

2003 backlog, 375 of 5,555 current majors (7 percent) and 2,131 of 36,033 

current individual minors (6 percent) were actually expired. Because the 

ePIFT data is updated quarterly for a known period of time, general permit 

data provided is not necessarily up-to-date. 

• Limits not updated in a current permit: All limits may not be up to date 

upon issuance of a current permit, which is not reflected in the measure. For 

example, some current permits are issued before a necessary TMDL and WLA 

37 
is available to limit discharges of impairing pollutants; however, while a 

WLA may not be available, the Agency indicated that pre-TMDL information 

could be incorporated into the permit. Also, permits may be updated but not 

the limits in PCS. New York’s administrative renewal process updates PCS 

dates but does not update limits in the permit. Also, permit tracking dates 

may be current but limits may be interim and not yet require compliance with 

final limits. 

• Permit quality: Permit quality problems could include lack of or 

miscalculation of a limit, possibly resulting in limits that may not be as 

protective of water quality standards. (See next section). 

However, some permits that are not current according to the backlog definition, 

and so do not appear to contain current limits, may not actually be causing 

negative environmental impacts. As noted in Chapter 3, although some facilities 

may not have a current permit, the facility may be discharging at rates that 

already comply with the revised limit once reissued. Therefore, the backlog 

measure of current permits may be confusing when correlated to environmental 

impacts. 

EPA Did Not Provide a Sufficiently Meaningful Explanation of Basis 

for Goal 

Although the 90-percent goal moves the status of the program forward from the 

baselines, EPA did not provide an environmentally or programmatically 

meaningful explanation of the basis of that goal. The level was set based on an 

assumption that there would not be a backlog if States and EPA maintained 

roughly a 20-percent rate of expiration and reissuance of permits annually; 

therefore, EPA assumed that a 10-percent backlog would equate to a 6-month 

backlog. However, the backlog measure does not reflect length of time in the 

backlog, and after 2002, all permits in the backlog are over 6 months old by 

definition. Although new permits are entering the backlog and others are being 

reissued, of the permits that could be analyzed, approximately 286 majors and 

2,293 individual minors found in the November 1998 backlog remained in the 

June 2003 backlog. This issue of long-delayed permits raises the question of 

when and how EPA should be involved in reissuing long-delayed permits, 

especially those impacting impaired waters, assuming EPA has the authority to 

take such action. 

Six of the eight States contacted believed the 90-percent goal was about right; 

one preferred the ability to fluctuate to a 30-percent backlog, and another 

believed 15-20 percent was more appropriate. EPA seems to be deemphasizing 

the goal’s definition by amending it to exclude permits backlogged due to 

rotating basin approach, adjusting for incomplete applications, and considering 

the possible affects from a new backlog measure. Although there are also 

concerns that the 95-percent priority goal may deflect achievement of the 

38 
90-percent goal, EPA accepts this possibility due to the focus on addressing 

higher priority permits that may take longer to reissue. 

EPA has already begun taking steps to improve the relevance of the backlog 

measure. It has, as previously described, developed the PER Strategy as well as 

the 95-percent priority permit goal, encouraged States and regions to use 

environmental significance criteria in selecting priority permits, continued to 

support a workgroup’s efforts to develop a checklist to evaluate environmental 

significance, and is asking regions to approve Permit Issuance Plans for any 

permitting authorities at less than an overall 70-percent issuance rate. Also, in 

conjunction with development of the State profiles, EPA is providing a 

Management Report for the NPDES permit program that includes the backlog as 

one measure among a number of others relating to program performance. 

Previously Reported Backlog Measure Could Have Led to Inefficient 

Results 

EPA and States are using the backlog measure in a number of management 

decisions: 

• Some States have adjusted where they allocate their resources. 

• Regions are using the measure for agreement negotiations with States, and 

most are also using it to gauge regional progress in the NPDES program. 

• Some regions are using it as an indication of the potential for environmental 

improvements. 

• Some regions use the measure when making resource decisions regarding 

funding or staff allocations and in directing funding to States. 

The backlog needed to be reduced for reasons including satisfying statutory 

requirements, improving oversight data, and addressing environmentally 

significant permitting issues. However, because of the uses of and attention on 

the measure of the backlog and its variable relationship to environmental 

outcomes, it may have unintended negative consequences, including the 

following: 

• Reduced quality: Pressure to reduce the backlog by expediting permit 

reissuances could negatively impact permit quality. A specific review of 

permit quality was outside our scope. However, challenges in about a third 

of authorized States show concerns regarding the effectiveness of the 

NPDES permit program. Further, EPA itself noted in its FY 2004 

Congressional Justification: 

39 
Recently completed permit quality reviews (PQRs) have also 

provided clear indications that the quality of those permits that 

are being issued is not what it should be to ensure that permits 

include requirements that result in achievement of water quality 

standards. Failure to address these problems of timeliness and 

quality may lead to additional withdrawal petitions or lawsuits 

against state NPDES programs. 

• Oversight lost: As discussed in Chapter 2, EPA has encouraged the 

increased use of general permits to address the backlog. However, because 

PCS does not provide sufficient information to track the backlog of facilities 

with general permits, let alone the environmental impact, EPA essentially 

loses oversight data for these facilities. EPA had to develop a separate 

database (ePIFT) to track summary data on general permit expiration. 

• Overall approaches can be disrupted: Overall permit management 

approaches can be disrupted by focusing only on backlog measure results. 

For example, while EPA is encouraging watershed or rotating basin 

management approaches to focus on environmental results, some States have 

had to address majors out of the basin sequence due to concentration on the 

backlog measures. Several States and regions commented that the emphasis 

on majors was no longer appropriate (see Chapter 3). 

• Resources may be inappropriately redirected: Because the measure does 

not include all NPDES permits, surface water permitting, or water quality 

management areas, managing to the backlog could result in redirecting 

resources from other areas that may be achieving equal or higher 

environmental results. For example, neither non-NPDES State permitting 

nor other activities addressing nonpoint source pollution are included in the 

backlog measure. Other important areas within the NPDES program, such 

as biosolids and significant aspects of the stormwater program, are also not 

included in the definition. EPA regions noted areas of potential 

environmental significance not included in the backlog definition, such as 

stormwater permitting, permit modifications, permit appeals, TMDLs, 

biosolids, industrial pretreatment, specific types of permits, general permits, 

new discharger/new sources, strategy and policy, permit quality guidance, 

and the old backlog having environmental and/or workload impacts. One 

State was even considering requesting to shift Federal resources from the air 

program to address the NPDES permit backlog. Decisions on resource 

allocations and potential shifts need to be informed by the relative resulting 

benefits of the activity. 

Backlog Measure Problems Affect Other Water Program Measures 

As noted, the NPDES permit program incorporates outputs of other Clean 

Water Act programs, such as effluent guidelines, water quality standards, and 

40 
TMDLs. Outcome-related measures for these programs assume or require 

implementation through an NPDES permit and compliance with the limits. 

Therefore, problems with the NPDES permit program, including the backlog, 

can have an adverse effects on expected outcomes for those other programs. 

The permit backlog and data issues relating to NPDES permits can affect other 

program outcomes reported in GPRA. Standardizing data on pollutants for 

water quality standards, TMDL listings, and NPDES permits – even if only on 

a State-by-State basis – would provide more usable information. Two program 

measures dependent on permits for enforceable implementation are: 

• TMDL measure: The actual accomplishment of EPA’s planned FY 2003 

GPRA measure of the number of approved TMDLs being incorporated into 

NPDES permits was not reported due to lack of available national data. This 

measure would have provided context for which backlogged permits on 

impaired waters were having a negative impact due to delayed permit 

issuance, which could have incorporated an existing WLA designed to 

correct the impairment. 

• Loadings reductions for effluent guidelines and NPDES program: The 

methodologies used to calculate loadings reductions from effluent guidelines 

for permits issued and for the permit program could be applied to the permits 

in the backlog to provide a similar outcome measure of estimated loadings 

reductions delayed due to the backlog. Although the permit and effluent 

guidelines programs are both designed to reduce loadings, permit limits may 

increase in response to increased industrial production or other factors. 

Reissuance of permits with increases and unchanged limits (identified in 

Chapter 3) should be incorporated into the overall loadings estimates or 

reported separately to provide accurate program outcome management 

information. 

* * * 

Conclusions and recommendations for this chapter are presented in Chapter 5, 

where they are integrated with conclusions and recommendations from other 

chapters. 

Agency Comment and OIG Evaluation 

EPA provided a number of comments regarding the discussion of the backlog 

measure both in its March 2005 response to the draft report and in discussion 

during the exit conference. Overall, with the development of the combined 

backlog measure and new baseline for FY 2005 through FY 2008 and the 

development of the PER related measure and goal for prioritized backlogged 

permits, EPA is addressing many of the concerns raised by the prior years’ 

GPRA reporting. EPA stated its intent was to give a more accurate picture of the 

41 
universe of permits and requested recognition of this or that the backlog estimate 

was not accurate because EPA knew of other universes that were not included. 

EPA noted that the most recent Federal Managers’ Financial Integrity Act 

(FMFIA) update recommends that the backlog no longer be an Agency weakness 

since mechanisms/processes are in place to assure timely water quality 

improvements through the NPDES program. EPA described the shift to 

emphasis on issuing priority permits (95 percent goal) along with the 

maintenance of the overall 90 percent current permits goal and the development 

of NPDES program profiles under the PER strategy to ensure the overall 

integrity/quality of the NPDES program. EPA also stated that it is important to 

note the ongoing efforts led by Office of Enforcement and Compliance 

Assurance to implement ICIS-NPDES (the replacement for PCS) will help all 

aspects of permit program management including permit issuance, compliance, 

and enforcement. EPA stated that this will further enhance their ability to 

improve the accuracy for GPRA reporting. 

EPA also requested several adjustments to our draft report to reflect information 

contained in backlog and FMFIA reports concerning the manner in which the 

backlog was being reported. EPA stated “[a]n integral part of the backlog 

reduction strategy was to determine the true nature of the backlog and workload 

through the cleanup of PCS data and inclusion of all facilities being permitted 

(addition of general permits information). Due to the nature of available 

databases and information collected, it was not practical to retroactively update 

the permit universe baseline because this changes month-to-month. Adding 

general permittees as part of the backlog changed the measure by expanding the 

universe of permits. This better represents the actual universe, and EPA 

acknowledges these changes in FMFIA, but it does not recalculate the baseline. 

Each of the refinements in the baseline was documented through FMFIA 

reporting.” 

We agree that the PCS data cleanup was necessary and recognize this change in 

our report as a necessary and valuable step in improving oversight of the 

program and management of the backlog. We also recognize that EPA has also 

established a new combined backlog measure and baseline in the FY 2005 

National Water Program Guidance. Further, a priority permit measure has been 

established designed to reflect environmental factors. 

While we recognize these improvements, our report also describes the historic 

backlog GPRA measure and reporting. Although the changes in the historic 

backlog data and measure are reflected in the section for “Verification and 

Validation of Performance Measures” of the Plan and Report documents, the 

associated reporting tables did not clearly represent this information. As of 

FY 2003 and 2004 reporting, the May 1999 baseline did not represent the same 

universe of permits for minors and did not reflect other significant changes such 

as the extension of time prior to backlog accounting and the cleanup of the PCS 

42 
data. However, progress in re-permitting facilities is overstated if measured from 

the original baseline due to subsequent changes in the definition of the measure. 

While the May 1999 baseline might not have been practical to update for the 

same date, it could have been replaced with a more representative baseline from 

October 2000. Even the new baseline data contains data that is known to need 

adjustment, including misreporting of 20,000 pipes as permits and different data 

entry approaches for two States. 

In addition, while ICIS may contain improvements that will lead to great 

accuracy for GPRA reporting, we were not able to confirm the final required data 

elements. The PCS modernization effort has encountered a number of delays 

and cost impediments. 

EPA further commented that the approach used by New York is being resolved 

through discussions between the State and EPA Region 2. EPA requested that 

the discussion section be removed and replaced with “EPA cannot recalculate the 

backlog because these permits are no longer expired but should work with New 

York to assure appropriate modifications are made and state clearly when 

discussing the backlog that New York has these modifications to accomplish.” 

We recognize that there are ongoing activities in New York and within EPA to 

resolve the issues highlighted in the draft report. We have not deleted all 

discussion of the topic in the report as this was an issue for about 10 years and 

impacted the accuracy of the backlog measure at the State and national level. 

Although we could not precisely quantify the impact, New York’s administrative 

renewal process inflated the backlog measure’s report of facilities with current 

permits. As we had noted, based on a State audit report in 2001, New York had 

encountered difficulty meeting its goal of reissuing 10 percent of its prioritized 

permits even though at this rate it would not be able to keep up with expiring 

permits (assuming an average of 20-percent permit expiration annually). Other 

issues identified that were not directly connected to the backlog included the 

limited opportunity for public comment for modifications as opposed to complete 

permit renewals and the use of a “short form” application. While administrative 

renewal will no longer be allowed for four specified permit categories, the 

deadline for full implementation of the program changes is October 2006. 

43 
Chapter 5

EPA Can Take Various Actions to Reduce 

NPDES Permit Backlog and Improve Water Quality 

EPA and States have taken various actions to eliminate the NPDES permit 

backlog, but can do more to address continuing and anticipated challenges. 

Further, because the NPDES permit program is not the only program involved 

with improving surface water quality, eliminating the backlog alone may not have 

a significant impact on improving national water quality. EPA and States need to 

balance efforts to eliminate the backlog with other efforts to improve water 

quality. Further, EPA needs to ensure that its efforts to reduce the backlog do not 

result in it quickly reissuing permits that are not as effective as they should be to 

improve water quality. Also, EPA needs to improve its reporting of the GPRA 

backlog measure. Due to the overlapping nature of the issues in Chapters 2 

through 4, we are providing overall conclusions and recommendations in this 

chapter. 

EPA’s Management of NPDES Backlog Highlights 

Importance of an Integrated Clean Water Program 

Since FY 1998, when the OIG and EPA identified the backlog of expired NPDES 

permits as a “management challenge” and “material weakness,” EPA oversaw a 

dramatic reduction in the size of the reported backlog. As a result, EPA and 

States are better positioned to address threats to water quality from point sources 

through the NPDES permit program. However, the backlog has not disappeared 

and some permits from the November 1998 backlog remained in the June 2003 

backlog. Further, significant numbers of facilities have been added to the NPDES 

program in recent years, and complex permitting issues have arisen, increasing 

workload and the potential for a large backlog in the future. 

The reduction of the backlog has also made visible other stresses on the permit 

program that hinder EPA’s achieving clean water goals. Challenges identified in 

this report include inadequate funding, ineffective communications, and 

organizational impediments. Although an NPDES permit is a program output that 

conveys enforceable means of protecting water quality, the ultimate goal of the 

NPDES program is maintaining and improving water quality through reduced 

discharges from point sources. Because program outputs may only be weakly 

associated with desired outcomes, improvements in measures of outputs, such as 

the size of the backlog, may provide only a muted signal of the extent of progress 

toward achieving environmental goals. 

The significant effort to reduce the size of the backlog, although important for 

improving overall management of the NPDES program, did not result in 

44 
significant water quality improvements. The backlog appears to be of limited 

significance as a national source of identified water quality impairments. A large 

majority of reissued major backlogged permits reviewed had at least one limit 

change or controlled a new parameter. However, reissued backlogged permit 

limits had varied environmental impacts based on the changes we were able to 

review while control of new parameters may be associated with greater 

environmental impacts. While we did not address the question of permit quality, 

our review indicated two key reasons why the backlog may not have significantly 

contributed to water quality impairment: 

• Significant discharge reductions may not have been needed upon permit 

reissuance because facilities adjusted operations in anticipation of a new 

permit or because additional permit limit adjustments will likely occur in the 

future as planned activities are undertaken by EPA in supporting programs. 

• A significant portion of the reported decrease in the backlog was due to 

administrative actions (such as removing backlogged permits by inactivating 

them) that, although necessary and important, did not directly affect water 

quality. 

Now that EPA has approached its backlog target, it needs to manage NPDES 

permitting to not only maintain and improve on achievements but, more 

importantly, ensure the needed steps are taken to achieve clean water goals. An 

NPDES permit is the product of a series of decisions made in relation to a variety 

of different programs. Whether the NPDES permit program is operating 

effectively is a very different, and more complex, question than whether 

90 percent of permits are current. Maintaining backlog targets involves permit 

streamlining and efficiencies, measurement of progress, and (more recently) 

issuing priority permits to achieve output goals of the NPDES program. 

To be confident that the NPDES program is achieving its environmental potential 

in achieving water quality goals, EPA needs to use an integrated approach rather 

than simply increase permit outputs. EPA needs to know if the NDPES program 

is supported not only by timely permit issuance but strong scientific and technical 

bases for limits, as well as compliance with limits, to promote clean and healthy 

ecosystems. EPA also needs the appropriate data systems to monitor how well 

the program is achieving goals, and the public and Congress need the right 

measure to hold the Agency accountable for progress in cleaning the nation’s 

waterways. 

EPA has begun new initiatives and approaches to address some of its future 

challenges. Improvements in communication, training, and collaboration among 

EPA and States will provide an additional boost to the NPDES program. The 

backlog may increase in importance as the other programs that support NPDES 

(e.g., water quality standards and TMDLs) increase in productivity. On the other 

hand, as EPA and States direct more attention to reissuing on time the more 

45 
significant backlogged permits, the environmental significance of backlogged 

permits may lessen. Although the net result of these changes on the backlog and 

the environment is unclear, it could very well produce a more effective and 

efficient permitting program that better protects water quality. 

EPA’s Steps to Improve Program Integration Need to Be Strengthened 

In the 2003-2008 Strategic Plan, EPA states, “progress toward water quality 

improvements will largely depend on success in integrating programs on a 

watershed basis; engaging diverse stakeholders in solving problems; and applying 

innovative ideas such as water quality trading, to deliver cost-effective water 

pollution control.” Through its PER initiative, EPA has demonstrated a 

commitment to improving the way that EPA and States manage the NPDES 

program. Beginning in 2004, the PER Strategy establishes a new vision for 

managing the NPDES program. EPA states that the PER Strategy's elements of 

integrity, efficiency, and environmental results will guide management into the 

future. The Agency is preparing management reports of the permit program, and 

has developed profiles of State programs. It has also announced that it is 

directing resources to address backlogs of water quality standards, and taking 

steps directed at TMDLs and permits. The new backlog measure based on 

priority permit issuance begins to integrate environmental concepts into the 

original, simpler metric. These potentially valuable steps are based on the 

concept of an integrated approach to addressing the backlog and managing the 

program for the future. 

EPA needs to build on the steps already initiated by improving management and 

oversight, strengthening communication and training, and improving performance 

measures. Although the challenges facing the NPDES program are complex and 

EPA has initiated actions, there are further steps that the Agency can take to 

reduce obstacles. Details on these issues are in Chapters 2 through 4, but the 

specific recommendations are presented in this chapter due to the overlapping 

nature of many of the issues. We believe that taking these steps will result in a 

stronger clean water permitting program that better protects the nation's waters. 

Recommendations 

To address NPDES permit backlog and overall program integration with the point 

source programs that support the permit program to achieve improved water 

quality, we recommend that the Assistant Administrator for Water direct staff to: 

5-1 Create a system for assessing the effectiveness and efficiency of the clean 

water program in achieving clean water goals by assessing the impacts of 

the activities – such as TMDLs, water quality standards, and effluent 

guidelines – that are designed to contribute to those goals. This would 

also aid the Agency in evaluating the impact of NPDES permit issuance. 

46 
EPA has already committed to doing this for the effluent guidelines 

program, stemming from a recommendation we made in an earlier report. 

5-2 Determine whether recently developed management reports included in 

the State profiles provide the full set of oversight information for the 

NPDES program. These should better facilitate management decisions in 

relation to the program and surface water quality in general. In addition, 

the measures in the management report specific to backlog management 

should also be addressed as follows: 

a. For the priority permits measure, EPA should study the effects of this 

approach and evaluate the progress toward the 95-percent goal. The 

study should determine if achieving this measure will assist EPA in 

achieving its overall watershed objective. It should also collect data to 

evaluate the 5-year permit period for nonpriority permits and any use 

of a priority factor that distinguishes between major and minor permits 

for prioritizing permit reissuance. 

b. For the current majors and minors measure, EPA should determine and 

describe the management information provided. For example, 

different criteria for the backlog may be appropriate to capture 

program integrity versus permits with current limits. Therefore, this 

description should consider State use of administrative renewals and 

other expedited reissuances, PCS data limitations, modifications, and 

TMDL-related permits reissued prior to the completion of a WLA. 

Also, in conjunction with the new focus on priority backlogged 

permits described in recommendation 5-2a, EPA should determine the 

percentage for the overall backlog where it will take action both on a 

national and State level. 

5-3 For the data needed to manage the NPDES backlog and integrate 

management of the permits program, ensure that systematic data 

collection is in place. EPA should evaluate the data quality and data input 

that support measures and management decisions, and develop a 

corrective action plan if deficiencies are identified. As EPA is in the 

process of revising the existing PCS Policy, which establishes mandatory 

data elements, any data needs (e.g., minors data, identification of water 

quality standards limits, etc.) for PCS should be incorporated where 

possible. 

To address the national NPDES permit backlog GPRA measures and 

management, we recommend that the Assistant Administrator for Water direct 

staff to: 

5-4 Ensure that the measure is clearly defined and the baseline is appropriate 

for the 2005-2008 GPRA measure (code 59) reported in the FY 2005-2008 

47 
Management System Matrix in the national guidance document. 

Specifically, EPA should: 

a. Clarify that the units of the baseline and measure include Federal as 

well as State permits. 

b. Determine the appropriate date and data for the baseline from which to 

measure changes. 

c. Not selectively remove permits from the measure without clearly 

explaining why permits are being removed and the effect on the 

measure. 

d. Provide a footnote for the baseline and measure describing the impact 

of New York’s permit management approach on the measure. This 

note may also be appropriate for backlog status reports posted on the 

internet. EPA could include reporting department-initiated 

modification rates until revisions in the administrative reissuance 

process to exclude certain permits would be reflected in the backlog. 

When this occurs is dependent on the expiration date of the permits, 

which may be several years in the future of permits. 

5-5 Determine whether EPA has the authority to reissue NPDES permits, 

particularly for facilities contributing to impaired waters, if the responsible 

State has not reissued a permit already expired for an extended length of 

time. 

5-6 Report an outcome measure for backlogged permits by applying the 

existing methodologies used to develop GPRA measures of loadings 

reductions for the NPDES permit program and effluent guidelines 

program. EPA should report the counterpart to the reported loadings 

reductions achieved by reporting the delayed loadings reductions 

associated with the applicable permits in the backlog. EPA should also 

review the loadings reduction models to ensure actual permit results, 

including reissued permits with limits that remain the same or allow 

increased discharges over previous levels. In a prior OIG report 

(Effectiveness of Effluent Guidelines Program for Reducing Pollutant 

Discharges Uncertain, Report No. 2004-P-00025 ), we also recommended 

that EPA develop effluent guidelines performance measures based on 

actual discharges rather than estimates. Finally, EPA should consider 

providing guidance to States about how to utilize the delayed loadings 

reductions calculated for backlogged permits (described in this 

recommendation) when they prioritize permits for reissuance. 

48 
To address the NPDES permit program and backlog management on a State level, 

we recommend that the Assistant Administrator for Water direct staff to: 

5-7 Work with Region 2 officials to complete review and revision of New 

York’s NPDES permit program according to the milestones shown in a 

July 2004 letter. In addition to New York’s agreement not to renew 

permits identified within four categories expected to require changes, EPA 

should take additional actions. First, EPA should also track department 

initiated modification rates of permits in the State. Second, EPA should 

work with the State to identify appropriate permits for prioritization of 

reissuance/modifications, including those identified within the four 

categories shown in the July 2004 letter. Finally, EPA should ensure that 

all appropriate categories for excluding permits from the renewal process 

are represented, including categories that may be appropriate for the future 

(e.g., permits that may be associated with new or revised water quality 

standards). EPA could consider a general statement regarding 

identification of other permits with permit limit or condition changes 

needed. 

Agency Comment and OIG Evaluation 

Overall, EPA agreed that addressing the backlog alone may not provide an 

effective strategy to improve water quality. The NPDES program is one part of 

the implementation of the Clean Water Act architecture. EPA acknowledged that 

permits in and of themselves do not protect water quality, but are a key element in 

the structure and the Agency's implementation of the Clean Water Act. However, 

the Agency requested that discussion of water quality impacts due to permit 

renewal be augmented to reflect the variety of ways in which permit renewal has 

an effect on water quality (for example, more stringent technology-based limits 

for existing permits, limits on new parameters, water quality-based limits, whole 

effluent toxicity limits, best management practices, improved monitoring 

requirements). EPA also recommended that the report recognize that overall 

program integrity (issuing permits as required by statutes) and pursuit of 

environmental improvements are both important. 

In response to our draft report’s statement on a need for proper balance for water 

quality programs, EPA stated that one dimension is the proper balance between 

the continuing effort to reduce the backlog as a program management goal and the 

need to ensure that the most environmentally significant permits are issued in a 

timely fashion. The permit prioritization effort initiated in 2004, under the PER 

Strategy, is intended to help the NPDES program strike the proper balance, and 

discussion of the prioritization effort would help clarify this issue. From the 

perspective of the Office of Water, sustaining an effective permitting program as 

the TMDL and standards programs continue to evolve is essential to the 

protection of water quality. 

49 
We acknowledge EPA’s comments that the NPDES program is just one aspect of 

the Clean Water Act programs and that, while key components in addressing 

point source pollution, permits do not in and of themselves address water quality. 

As a result, addressing the backlog alone may not have significant impacts on 

overall water quality. We agree with EPA’s comments regarding other aspects of 

permit renewals that have potential impacts and included information in Chapter 

3. We also agree with EPA’s comments regarding the backlog measure reflecting 

program integrity efforts and added information in Chapter 4. Further, we agreed 

with EPA’s comments on balancing reduction of the backlog with the need to 

address environmentally significant permits. Information addressing the PER 

Strategy and prioritization measure has been added throughout the report. 

EPA also provided comments regarding the draft recommendations. EPA 

indicated that it will be able to address the intent of the recommendations via its 

prospective approach to managing the NPDES program as embodied in the PER 

Strategy and the Office of Water Strategic Plan. EPA stated that a number of the 

steps suggested have already been initiated. EPA also provided specific 

comments that have been incorporated to clarify recommendations and, in some 

cases, resulted in re-numbering of the recommendations due to deletion or 

combining. 

As EPA informed us that permit-specific information is not submitted for each 

permit on the priority permit list, we have modified the draft recommendation 5-1 

but still encourage the use of information to help evaluate the effectiveness of 

“feeder programs.” Information on which programs are or are not generating 

outputs leading to permit limit changes on a State basis could generate valuable 

management information from the permit program for those feeder programs. We 

encourage EPA to continue to use PER and its integrity component as well as 

other data sets available to assess the effectiveness of feeder programs – such as 

water quality standards, effluent guidelines, and TMDLs – on NPDES permit 

limit changes and discharges. EPA should prioritize permits for reissuance and 

continue taking whatever steps feasible to better integrate the various programs 

on a watershed basis in order to ultimately improve surface water quality as 

described by EPA in the 2003-2008 Strategic Plan. 

EPA recommended that several of the recommendations that relate to measures in 

the Management Report should be consolidated. We agreed and consolidated 

draft recommendations 5-9 and 5-10 regarding measures in the final 

recommendation 5-2. 

EPA commented that draft recommendation 5-3, which addresses data issues, be 

revised. EPA stated that “[b]ecause we have revised ICIS and Ask WATERS to 

address our needs, the issue that remains is data quality and data input. We 

suggest this be reworded to focus on this.” We agreed that the recommendation 

should be clarified to address data elements and not data systems and revised the 

recommendation accordingly. 

50 
Draft recommendation 5-4 dealt with GPRA reporting. EPA recommended that 

we state that the GPRA baseline needs to reflect a PCS retrieval correction for a 

Region 6 Oil and Gas Permit that inadvertently counted pipes, inflating the 

number of permits. With the correction, the baseline is expected to decline by 

about 20,000 permits. For the issues related to New York, EPA suggested this be 

reworded to capture that permits which should have been modified in New York 

be added to the priority permit list for New York. We agree with EPA that the 

baseline for the revised 2005 backlog measure may not be accurate and revised 

the recommendation to reflect the need for an accurate baseline. 

EPA agreed with draft recommendation 5-5 and indicated they were already 

taking action. EPA is holding a conference in September and has had monthly 

conference calls all year. Regarding draft recommendation 5-6, EPA requested 

the recommendation be deleted since States request training and help determine 

location and frequency, and because EPA provides several types of training. EPA 

is also in the process of developing online training modules for deriving water 

quality-based effluent limits and may consider adding other aspects of the NPDES 

program to the web-based tool. Based on the information provided in comments, 

the exit conference, and other followup regarding ongoing activities, we deleted 

draft recommendations 5-5 and 5-6. 

EPA provided no comments on draft recommendation 5-7 and it is unchanged. 

Regarding draft recommendation 5-8, EPA reported that Region 2 and New York 

are addressing the issue as a result of the PER review. EPA requested that this 

recommendation be deleted as New York has agreed and is revising this program 

in response to a letter from Region 2. Due to the importance of proper 

implementation of the NPDES program in delegated States and about 10 years 

passing before final EPA review, we are not deleting the recommendation but are 

revising it to reflect the milestone dates agreed to by the State and Region 2. EPA 

should continue efforts to meet milestones described in a July 2004 letter from 

New York to Region 2. The milestones are based on a draft work plan to be 

submitted by February 2005 with associated interim approval milestones; by 

September 1, 2005, EPA is expected to approve the program and public 

participation should be initiated in New York. Program changes should be 

finalized and implemented by New York as of October 1, 2006. 

Regarding recommendations 5-9 and 5-10, which we consolidated into 

recommendation 5-2, EPA also requested that draft recommendation 5-10 be 

revised. EPA requested that the aspect regarding major and minor permits be 

deleted since EPA combined its goal for 2005. While we recognize that EPA 

combined the measure, as the distinction between major and minor permits may 

impact prioritization of reissuance, we did not delete this aspect of the 

recommendation. EPA suggested that the recommendation for an evaluation 

should be combined to capture whether they are measuring the right things to 

achieve the watershed objectives and have the right emphasis. EPA also 

51 
suggested that we consider instead that EPA may want a backlog goal focused on 

10 years for non-priority permits and retain the priority permit goal for 

environmental significance and evaluate if it is working. Finally, EPA suggested 

that we might also want to include if EPA should consider areas needing a TMDL 

or standards to be more clearly excluded from the backlog so as to not create a 

disincentive for more holistic approaches. We revised the recommendation to 

reflect that prioritizing permits for reissuance should support EPA’s watershed 

initiative. This is important because of a continued need for additional overall 

integration of programs such as water quality standards and permits and 

allocation of associated resources according to water quality impacts and not 

based solely on the backlog measure. We did not further revise the 

recommendation although we generally agree that EPA may want to consider 

different approaches for non-priority permits, such as a process for streamlined 

renewal, but recognize that the possibility of changes within a 10-year period may 

require adjustments of permits to reflect new environmental requirements; the 

ability to reopen a 10-year permit could be critical. EPA may want to evaluate 

supporting programs before considering a 10-year permit period. 

Finally, EPA recommended that draft recommendation 5-11 include the statement 

"or include loadings in permit prioritization." We generally agreed with EPA’s 

recommendation, but added it as a separate action and not as an alternative. We 

also clarified the wording of the recommendation. EPA’s current loadings 

methodologies allow for an estimate of the amount of loadings reductions delayed 

that are associated with backlogged permits. This information may be useful to 

the Agency and States in prioritizing permit modifications and reissuance efforts. 

52 
Appendix A 

Details on Scope and Methodology 

Surveys and Field Visits 

Separate survey instruments were developed to obtain information regarding the NDPES permit 

backlog. A total of no more than nine States received each set of questions. Information on 

selection criteria and participation is presented below for collection of causes of the June 2003 

backlog and backlog management by States and EPA: 

• Causes of Backlog - State and EPA: We collected this data to obtain information on the 

causes affecting the largest percentage of the national backlog, and it was not generated to 

represent an individual State’s or EPA region’s high backlog percentages. All EPA regions 

with backlogged permits in the status report as of June 2003 received this question as well as 

nine States (Illinois, Louisiana, Mississippi, Missouri, Nebraska, New Jersey, Ohio, 

Pennsylvania, and West Virginia). State selection was based on individual permit backlog 

statistics on a State basis (regardless of the percentage of current permits in the State); 

several States were excluded because they are not authorized for the program. Seven States 

responded (Illinois and Louisiana did not submit a response), and completed surveys were 

aggregated and analyzed. 

• EPA and State Management of Backlog: A separate backlog management survey was sent 

to eight states (Colorado, Indiana, Kentucky, Michigan, New York, North Carolina, 

Washington, and West Virginia), and a version specific to EPA sent to all EPA regions. 

Originally, we selected nine States using criteria designed to identify States representing a 

range of experiences (successes or challenges) in managing the backlog. However, Oregon 

was removed from the selection based on ongoing studies in the State. The selection was 

made based on backlog changes shown in the status reports between April 2001 and 2003. 

Several States were not considered for selection because the State was not authorized for the 

program or because of the size of the permit universe. Completed surveys were aggregated 

and analyzed. We also conducted on-site interviews during field visits to five of the States 

(Colorado, Michigan, New York, North Carolina, and Washington) identified for the 

management questionnaire and five of the regions (Regions 1, 3, 6, 8, and 10). 

Data Analysis in PCS and Other EPA Systems 

We also used PCS data to analyze the permit backlog based on the permit’s backlog status as of 

June 2003, with some updates as of March 2004. We consulted the Government Accountability 

Office report Assessing the Reliability of Computer-Processed Data (GAO-03-273G, October 

2002, external version 1). We used the same definition and data set used and reported on by 

EPA in the backlog status reports. However, in analyzing permit limit changes, we used the 

original permit backlog delay allowance of 45 days to generate data for the June 2003 backlog 

analysis. Permit limit data and discharge monitoring report data were downloaded at a later date 

53 
and analyzed in IDEA software. The last modified permit limit in the prior permit was compared 

to the original limits in the new current permit. Limit analysis did not include flow data or 

records with changes in unit codes. Records in the prior and current permit were matched using 

a key made of elements from PCS: 

Permit Number + Pipe Discharge Number + Report Designator + 

Limit + Parameter + Monitoring Code + Season Number 

In a final step, we compared available data for these limits showing the time frame for the limit 

(e.g., monthly, weekly, or daily limits). Because this data is not required, we can only provide 

information where these were not identical if provided. This may contribute to some additional 

uncertainty in identifying limit changes in reissued permits. 

We also analyzed current permit records with final limits that did not match against a ghost 

permit record following the same data screening process. These records were not analyzed for 

limit changes but were analyzed to identify why the record did not match: no prior permit; a 

new parameter was being limited; or the monitoring location, pipe discharge number, or season 

code did not match. 

PCS is an official EPA database used for enforcement and reporting purposes. However, based 

on data concerns raised in prior OIG, EPA, and Government Accountability Office reports on 

PCS, we performed targeted data reliability testing. Although some errors were identified, they 

did not appear to significantly affect the overall analysis, particularly when other existing data 

sources and questionnaire information were also used. The data we considered to be most 

unreliable for a particular analysis has been eliminated throughout the analysis. PCS data in this 

analysis was generally limited to permit expiration dates and facility data, and for majors limits 

and a small set of discharge monitoring report data. We also reviewed Water Enforcement 

National Data Base (WENDB) elements (EPA identifies as core information necessary to use 

PCS to conduct oversight of the effectiveness of the NPDES program). We believe that, overall, 

the reliability of screened data in conjunction with other data is sufficient for the level of 

conclusions drawn. A review of permit quality (calculation of permit limits) or compliance and 

enforcement information was outside the scope of this study. We also did not perform data 

quality reviews on discharge monitoring report data. 

Because prior permit tracking dates are overwritten in PCS when permits are reissued, we used 

the permit limit start and end dates of “ghost” permits (also known as “prior” permits) in PCS for 

this analysis. When multiple permit limit start and limit end dates were identified in a single 

permit’s data due to interim limits and modifications, we placed the permit in the lowest age 

category (newest) identified. However, we used the data for each record as presented in PCS 

and the associated age category without any adjustment as described above to identify permits in 

the lowest age category. This may contribute some additional uncertainty to identification of 

permit limit changes for the backlog (permits not reissued for over 45 days). 

We obtained discharge monitoring report data for quantity maximum and average limits that 

decreased when they were reissued for the time period of the limit start and end date for the limit 

in the prior permit. Any limits where data were available in PCS for both the prior and current 

54 
permit and which indicated a change in the timeframe of the limit (e.g., daily, weekly, or 

monthly) were removed from the analysis. Each value obtained was compared to the prior limit 

as well as the current limit. At this detailed level of analysis, we also adjusted the backlog 

definition date from 45 days to 180 days for those permits issued after January 2002 to match 

EPA’s definition changes for the backlog. 

To estimate the number of impaired waters associated with a backlogged or expired permit, we 

used different data sets of expired permits identified on impaired waters. The preliminary Office 

of Water data analysis identified backlogged permits as of March 2004 (expired in September 

2003). The Office of Enforcement and Compliance Assurance analysis used expired permits 

data extracted in February 2004. Due to the different focus on expired and backlogged permits 

in the two data sets, the time frames are slightly different. We analyzed both sets of data to 

develop a range of estimates. First, we estimated the number of waters associated by point 

sources according to available estimates using the April 2004 303(d) listing of 26,209 impaired 

waters (60 percent of these is approximately 15,725 water segments). We divided the number of 

waters estimated by EPA to be affected by point sources by the total number of expired permits 

identified on impaired waters in the different data sets. This provided a range of estimates of 

impaired waters that could be associated with expired or backlogged permits. We also 

calculated a higher number of waters per backlogged permit because the data sets showed less 

than 15,725 permits (current or expired) as being on impaired waters. Therefore, we calculated a 

higher estimate of impacted impaired waters by dividing the estimated number of waters 

impaired by point sources by all known individual permits and multiplying the resulting ratio 

with the number of backlogged permits. We recognize that this range may be an over- or underestimate because general permitted facilities are not included in EPA’s analysis, some waters 

may not be affected by point sources, and not all permits have been georeferenced. If the 

backlogged permit already incorporates a TMDL WLA, or if there is no approved TMDL WLA 

for that permit, the backlog status of the permit is not likely to be a contributing factor for the 

impairment because resolution of the impairment is dependent on the TMDL. EPA comments 

indicate that TMDL WLAs are not needed before a permit limit may be developed. If they are 

available, they are to be considered. 

Prior Reports 

The OIG has issued several reports addressing issues related to the NPDES permit program, 

including: 

• Congressional Request Regarding EPA Clean Water Enforcement Actions, 

Report No. 2005-S-00001, October 18, 2004. 

• EPA Needs to Reinforce Its National Pretreatment Program, Report No. 2004-P-00030, 

September 28, 2004. 

• Effluent Guidelines Program for Reducing Pollutant Discharges Uncertain, 

Report No. 2004-P-00025, August 24, 2004. 

• EPA Should Take Further Steps to Address Funding Shortfalls and Time Slippages in Permit 

Compliance System Modernization Effort, Report No. 2003-M-00014, May 20, 2003. 

55 
The OIG also issued two reports in 1998 that specifically addressed the backlog issue by 

identifying a number of NPDES permits that had not been issued or reissued in a timely manner: 

• Kansas National Pollutant Discharge Elimination System Program, 

Report No. E1HWF7-07-0022-8100089, March 31, 1998. 

• Region 10's National Pollutant Discharge Elimination System Permit Program, 

Report No. E1HWF7-10-0012-8100076, March 13, 1998. 

Further, since 1998, the OIG has reported the NPDES permit backlog as a Management 

Challenge for the Agency. 

We also identified a number of State-specific reports addressing NDPES permitting and backlog 

issues. Examples follow. 

• A Minnesota report, Progress Report, Wastewater Point Source Permitting, Compliance and 

Enforcement, February 2003. 

• A New York State Auditor’s report, Clean Water Permit Process, Report 2001-S-18, 

March 13, 2003. 

• A National State Auditors Association Joint Performance Audit, Water Quality, August 2001. 

56 
Appendix B 

Definitions and Examples of 

Alternatives to General Permitting 

Permitting by Rule 

“Cookie Cutter” Permits 

Provides for automatic coverage of facilities, but is time-consuming to complete 

(used mainly for stormwater permitting but is being considered for other discharge 

types in several States). 

Use basically the same permit format with small variations. 

Reauthorized Permits Require identification by ranking of permits that will have no substantive changes 

upon reissuance (no changes to previous permit except for submittal dates, and 

new cover page with new signature and effective and expiration dates). 

Reduced Effort Permits Wisconsin has been working on guidance for permits that can be reissued without 

an in-depth review because the discharge is not causing or does not have the 

potential to cause a significant environmental problem based on determining 

factors (e.g., low environmental concern, strong compliance history, and no 

significant changes in facility operations). EPA Region 5 identified this practice as 

a particularly successful State activity for addressing the backlog. 

Expedited Permits Require identification of permits with simple or no changes that can be addressed 

by less experienced staff. 

Batch Permits Minnesota identified and “batched” similar types of permits in the backlog, which 

streamlined the process by using common boilerplate language and application of 

laws, rules, and standards. Region 5 also identified processing certain permits in 

Indiana in batches as a particularly successful practice. 

Roll-over Permits An identification by certification of no change could allow permit issuance without 

pre-permit inspection. 

57 
Appendix C 

Changes in Permit Limits 

Permits (% of total), 

Based on 2,235 Permits, 

Except Based on 2,681 Where 

New Parameters Also Counted Records 

Facilities/records with a current (major) permit 

and a previous backlogged permit in matching 

analysis (only in exceptions analysis) 

2,476 

plus 205 (only in exceptions 

analysis equals 2,681) 

51,569* 

(plus exceptions 

analysis records for 

new parameters 

equals 59,381) 

Facilities/records with a limit change or new 

parameter 

 Facilities/records with a limit change 

 Facilities/records with a decreased limit 

 Facilities/records with a new parameter 

Facilities/records with a limit increase 

2,166 

1,748 

1,080 

1,384 

1,079 

17,717

9,905

3,631

7,812 

3,959

 Facilities/records with additional new

 limits for previously controlled pollutant 

1,110 3,936 

Facilities with no new limit or new parameter 

and records with no limit changes (not 

corresponding to the more limited permits) 

515 39,870 records with 

no limit changes 

Could not be matched and were not a new 

parameter (not included in the total number of 

analyzed records) 

1,353 permits 

(permits may have records 

in matching or exceptions 

analysis) 

12,926 records 

(not included in 

52,634 total above) 

* Total number of records in analysis except for records with deleted limits (after removing likely errors and flow 

parameters. 

Note: Permits and records may overlap. Included in the table are 9,061 records in 1,113 permits that had changes in

parameter units between the prior and current permit that were analyzed using standard limit data. About 8 percent of

analyzed records (including up to 5 limits per record) indicated a change in the unit of time for reporting, which should

be considered as an uncertainty in conclusions drawn from this data. 

Limit Changes Identified:

Decrease: A negative value is obtained if the prior limit is subtracted from the current limit.

Increase: A positive value is obtained if the prior limit is subtracted from the current limit. An increase may be a more

stringent discharge limit in the case of select parameters such as dissolved oxygen, temperature, and pH.

Stay the same: There was no change in the permit limit between the prior and current permit limits.

Additional new limit: A permit limit record consists of up to five limits per record (row). A new additional limit was

identified where a controlled pollutant also had a different limit type that was blank (or a monitoring limit), which

became a final limit in the current permit. 

New parameter with a final limit: These are final limits in a current permit for a parameter that did not have a final

numeric limit in the prior permit. 

Deletion of limit: The deletion of a limit was not considered a change.

58 
Appendix D 

Factors That Indicate a Permit Likely to Have

New Limits or Conditions When Reissued

 General categories of factors in addition to those identified in EPA’s draft checklist that regions note as

 likely to cause a permit to have a new limit or condition when reissued. 

Receiving waters (e.g., dilution, changes in flows, watershed planning) 

Water quality standards (e.g., downstream State considerations and new designed uses) 

Study data (e.g., mixing zones and effluent monitoring results) 

Reasonable potential analysis 

Sanitary Sewer Overflow conditions after EPA actions 

Implementing Toxicity Identification Evaluation/Toxicity Reduction Evaluation results after 

Whole Effluent Toxicity (WET) testing failures 

New regulations implementing Clean Water Act section (e.g., 316(b), addressing cooling water intake 

structures for new facilities) 

Lower detection limits due to new, EPA-approved analytical methods 

Oldest backlogged permits that are usually delayed due to old issues 

59 
Appendix E 

Universe of Permits Counted in Backlog

and Number of Current Permits

(Selected Dates, 1998-2004)

November 1998 

(except as 

otherwise noted) June 2003 March 2004 

Change in Current and 

Universe of Permits from 

November 1998 to: 

June 2003 March 2004 

MAJORS: Current 5,017 5,555 5,606 +538 +589 

Universe 6,808 6,675 6,700 -133 -108 

INDIVIDUAL 

MINORS: 

Current 33,714 36,033 34,167 +2,319 +453 

Universe 64,702 45,419 42,179 -19,283 -22,523 

ALL MINOR 

FACILITIES: 

Current 87,790 * 80,108 81,195 -3,682 -2,595 

Universe 103,711 * 96,006 93,561 -7,705 -10,150

 * “All Minor Facilities” data generated October 2000, not November 1998. 

60 
Appendix F 

Agency Comment 

Memorandum 

SUBJECT: Draft Evaluation Report: "Efforts to Manage Backlog of Water Discharge 

Permits Need to Be Accompanied by Greater Program Integration." 

FROM: Benjamin H. Grumbles 

Assistant Administrator 

TO: Dan Engelberg 

Director of Program Evaluation, Water Issues 

Office of Program Evaluation 

Office of Inspector General 

Thank you for your memorandum dated January 25, 2005, transmitting the draft report 

on the subject evaluation, No. 2002-000221. The draft report provides a useful overview of the 

substantial efforts by EPA and the States during the last seven years to respond to the backlog of 

NPDES permits that developed during the 1990's. 

We have a number of recommendations for changes to the draft report that we believe 

would improve its clarity and accuracy. The Office of Water's key recommendations are 

summarized here, while more detailed suggestions are provided in the attachment. 

1) Implementation of Permitting for Environmental Results (PER) Strategy - Beginning at 

the outset of 2004, the PER Strategy establishes a new vision for managing the NPDES program. 

It is the PER Strategy's elements of integrity, efficiency, and environmental results will guide our 

management into the future. In order to convey to the reader a more complete picture of the 

NPDES program, the report should emphasize the role of implementation of the PER Strategy in 

addressing overall permit program effectiveness, particularly with respect to water quality 

improvements. The implementation of the Strategy is likely to have impacts in the area of 

permit issuance efficiency and the environmental importance of those permits that are renewed. 

This discussion should be moved up front and included in the "At a Glance" section and Chapter 

1. 

2) Impact on Water Quality from Permit Renewal, and Balance in the Permitting Program 

and between Related Water Quality Programs -- The conclusion in the "At a Glance" section 

and discussed at some length in Chapter 3 that the backlog reduction has had a limited impact on 

water quality is one that we believe needs to be reexamined. To reach this conclusion, the 

report relies on an analysis of DMR results on existing limits from a small subset (12% of the 

sample) of reissued permits The discussion in this area should be augmented to reflect the 

variety of ways in which permit renewal has an effect on water quality (for example, more 

61 
stringent technology-based limits for existing permits, limits on new parameters, water 

quality-based limits, whole effluent toxicity limits, best management practices, improved 

monitoring requirements). Overall, we agree that backlog alone may not provide an effective 

strategy to improve water quality as is stated later in the report. The NPDES program is one part 

of the implementation of the Clean Water Act architecture. We acknowledge from the outset 

that permits in and of themselves do not protect water quality, but are a key element in the 

structure and the agency's implementation of the Clean Water Act. 

Further, the draft report raises the question of the proper balance for water quality programs in 

several places. One dimension is the proper balance between the continuing effort to reduce the 

backlog as a program management goal and the need to ensure that the most environmentally 

significant permits are issued in a timely fashion. The permit prioritization effort initiated in 

2004, under the PER Strategy is intended to help the NPDES program strike the proper balance, 

and discussion of the prioritization effort would help clarify this issue. 

The draft report also raises questions about the right balance between the various water quality 

programs (principally TMDL and water quality standards). State and regional authorities are 

given flexibility in timing of permit re-issuances while TMDLs, new standards, or new 

approaches (for example, watershed-based permitting) are being completed. From the 

perspective of the Office of Water, sustaining an effective permitting program as the TMDL and 

standards programs continue to evolve is essential to the protection of water quality. 

We believe the analysis of potential impacts to water quality would be better framed using the 

chart in Appendix C. The analysis examines permit limits and changes to limits over time, but 

omits very important parts of the permit program universe, such as control of storm water and 

control of indirect discharges through the pretreatment program. The overall discussion should 

address the limitations of the analyses in more detail. 

3) Impact from Implementation of Effluent Guidelines - The report should give greater 

recognition to the impact that implementation of effluent guidelines promulgated in the last 

decade or more will have on water quality as we continue to implement the NPDES program. 

Permits that were last updated 6, 8 or 10 years ago will not reflect the improved 

technology-based limits that are contained in the guidelines promulgated during the 1990's and 

earlier in this decade. Two prominent examples of guidelines that are expected to have a 

substantial impact are the 316(b) rule and the CAFO regulations. 

4) Backlog, Permit Universe and FMFIA Reports - Several adjustments should be made to 

reflect information that was contained in Backlog and FMFIA reports concerning the manner in 

which the backlog was being reported. An integral part of the backlog reduction strategy was to 

determine the true nature of the backlog and workload through the clean up of PCS data and 

inclusion of all facilities being permitted (addition of general permits information). Due to the 

nature of available databases and information collected, it was not practical to retroactively 

update the permit universe baseline because this changes month-to-month. Adding general 

permittees as part of the backlog changed the measure by expanding the universe of permits. 

This better represents the actual universe, and EPA acknowledges these changes in FMFIA, but 

62 
it does not recalculate the baseline. Each of the refinements in the baseline was documented 

through FMFIA reporting. 

The most recent FMFIA update recommends that the backlog no longer be an agency weakness 

since mechanisms/processes are in place to assure timely water quality improvements through 

the NPDES program. These include the shift to emphasis on issuing priority permits (95% goal) 

along with the maintenance of the overall 90% current permits goal and the development of 

NPDES program profiles under the PER strategy to ensure the overall integrity/quality of the 

NPDES program. 

It is also important to note the ongoing efforts led by OECA to implement ICIS-NPDES (the 

replacement for PCS) that will help all aspects of permit program management including permit 

issuance, compliance and enforcement. This will further enhance our ability to improve the 

accuracy for GPRA reporting. 

We recommend that the report recognize that overall program integrity (issuing permits as 

required by statutes) and pursuit of environmental improvements are both important. 

5) Recommendations Section - Regarding the recommendations, we will be able to address the 

intent of the recommendations via our prospective approach to managing the NPDES program as 

embodied in the PER Strategy and the Office of Water Strategic Plan. A number of the steps 

suggested in Chapter 5 have already been initiated. In the case of the New York State 

Department of Environmental Conservation (NYSDEC) system, we are able to report that 

Region 2 and NYSDEC are addressing the issue as a result of the PER review. After discussing 

the issue with NYSDEC, the Region sent a letter stating that NYSDEC needs to modify their 

system to address the issue. Finally, we believe a number of the remaining recommendations 

should be consolidated. 

The attachment provides specific comments on each of the chapters of your draft report 

for your consideration. If you have questions about any of our comments, please contact Linda 

Boornazian, Director, Water Permits Division, at (202) 564-0221 or Tom Laverty, Chief, 

State/Regional Branch at (202) 564-7974. 

63 
Attachment - Chapter-by-Chapter General and Specific Comments on the -

Draft Evaluation Report: "Efforts to Manage Backlog of Water Discharge Permits Need 

to Be Accompanied by Greater Program Integration." Assignment No. 2002-000221 

January 25, 2005 

At a Glance 

General Issues 

This section makes many very broad statements that seem generally connected to the idea 

of integration and looking holistically at water quality management. Given this broad 

discussion, we recommend including the fact that we have undertaken a very holistic approach to 

dealing with management of the NPDES program. As discussed in the memo transmitting these 

comments, we feel the Permitting for Environmental results (PER) strategy is the correct 

approach for dealing with backlog as part of a much larger program management approach that 

focuses on performance. This holistic approach has included looking at the water quality 

standards program, technology standards program, water quality assessment program, permits 

program, and enforcement program together. This has provided a much better data set from 

which to make decisions about appropriate approaches to water quality management. 

Specific Issues 

In the 3rd paragraph of this section, the statement is made that "the backlog could grow in 

importance if supporting programs are strengthened." Given the focus of this report, and the 

data collected and analysis performed, it is not clear that this very broad generalization can be 

supported. 

In the 4th paragraph, the report indicates that GPRA reporting has provided a misleading 

view. We do not think this is accurate. When definitions were changed we always provided 

explanation for the changes. Baselines were changing due to cleanup, migration to general 

permits, and new permittees coming on line. Year-to-year measures reported in our Annual 

Report are covered in more detail later in our comments. 

Chapter 1 - Introduction 

General Issues 

The first sentence does not accurately reflect current work within the NPDES program. 

Specifically, it can be read to completely ignore the large amount of work being done as part of 

the Permitting for Environmental Results (PER) program. We recommend the Introduction be 

64 
changed to reflect the fact the analysis done for this report "focused" on the issue of backlog, and 

therefore, did not fully consider the impact of ongoing work being done as part of the PER 

program. 

Specific Issues 

In the section devoted to Background, the first sentence is inaccurate; the Federal Water 

Pollution Control Act was "originally" established in 1956. We suggest changing the sentence to 

read, "Congress established the NPDES program through the 1972 amendments to the Federal 

Water Pollution Control Act. 

In the section devoted to "Backlog of Expired Permits Identified," the first paragraph 

needs to explain the re-issuance process. The explanation should include requirements in 40 

CFR 122.21 related to applying and re-applying for a permit, as well as section 122.6 that deals 

with continuation of permits and the link to re-applying. 

In this same section, in the next to last paragraph, mention is made to the changes to the 

definition of backlog. This issue also comes up later in the report. We recommend noting that 

each time a definition changes was made, the change was noted in the FMFIA report and in the 

report we recognized the need to clean-up the data and process for tracking backlog. It should 

also be noted that we reached a consensus with permitting authorities only as backlog 

management evolved that facilities covered by non-storm water general permits should be 

included in the backlog accounting inventory. With the implementation of PER, the definition 

of backlog now includes facilities covered by individual (majors and minors) and non-storm 

water general permits. The report should state that capturing these permittees in the backlog 

accounting provides a better measure of the permit issuance realities faced by a permitting 

authority. Because our tracking effort has understandably evolved over the years, the report 

should further note that it is not practical to go back in time and make adjustments to the baseline 

rather we should continue to improve explanations in the annual reports and make adjustments to 

the GPRA measures where feasible It should also state that Regions and States started using 

more general permits so a more accurate picture of facilities without current permits would not 

be accurate if only individual permits were counted. 

EPA's intent was to give a more accurate picture of the universe of permits. This report 

should recognize this or one could say that the backlog estimate wasn't accurate because we 

knew of other universes that weren't included. 

The level of backlog has two perspectives: good program management and quality of 

permit. Permittees have complained to us (most recently in a meeting for performance track 

facilities in September, 2004) when their permits are not issued in a timely manner because it 

promotes the notion that the permitting authority is not responsive or sends a negative message 

to their community or their stockholders or board of directors. Permit quality reflects the 

appropriate level of control has been included in the permit to maintain or improve water quality, 

including necessary water quality controls or technology-based controls (effluent guidelines). 

The second point is discussed fairly well, but the first is not recognized. 

65 
Chapter 2 - Management of Backlog Improving But Challenges Continue 

General Issues 

EPA concurs that resource constraints hamper a permitting authority's ability to meet 

permitting goals. Declining State resources are one of the most problematic issues facing 

permitting authorities and, as noted in the OIG report, many permitting authorities have stepped 

up to the challenge using various approaches to increase efficiencies. 

EPA is working to help States improve efficiencies and integrity through the use of 

permitting tools and working as facilitator, developer, and collaborator on electronic applications 

to assist permitting authorities improve the quality of permits while improving efficiencies. We 

are increasing our outreach efforts regarding electronic tools in 2005. EPA established a Clean 

Water Act 104(b)(3) cooperative agreement with the Association of State and Interstate Water 

Pollution Control Administrators (ASIWPCA) to collect and share good strategies and practices 

among states as well as participate in the PER process. 

Regarding communications, EPA uses several channels: 

! ASIWPCA Monthly Calls 

! Permit Writers Courses (Five per year in different locations based on consultation with 

states and regions to determine locations with greatest need) 

! Permit Writer Practitioner Meetings (every two years) 

! Permittee Training Courses with Water Environment Federation (3 to 4 per year) 

! Comprehensive web site (www.epa.gov/npdes) with additional training in specific 

program areas 

! Periodic meetings between states and EPA regions, including state program reviews by 

the regions 

! Participation in meetings with States through ASIWPCA 

! National Meeting with States and Regional NPDES managers is planned for September 

As an outcome of the PER process, EPA will be able to identify opportunities to further 

assist permitting authorities to improve their permitting programs. In particular, the priority 

permits program addresses some of the concerns of the OIG, where permits are linked to 

environmental or other administrative criteria. 

Based on this information, we believe that Recommendations 5 and 6 in Chapter 5 should 

be removed because these actions are underway and already mentioned as important in an earlier 

chapter. 

Specific Issues 

In the first 2 paragraphs under the Resource Constraints section, there is reference to 

survey results. In the first paragraph, the results were from 6 of the 7 states and in the second 

paragraph the results were from 6 of 8 states. We assume this is based on respondents as 

66 
opposed to actual population surveyed. We suggest explaining why different numbers of states 

were surveyed given the methods section indicated that 15 states were surveyed. 

In the section: Workload Management Approaches, under "Alternatives to Traditional 

Individual Permitting," the fourth bullet can be read to discourage using statewide general 

permits when a rotating basins approach is used. Why do you feel this is inappropriate? The 

State of Michigan has indicated they are experiencing a lot of success with this hybrid approach. 

In the section: States and EPA Must Address Increasing Complexities, in the first bullet 

there is some discussion of variances. Variances by definition are short-term modifications of 

water quality standards. Therefore, the variance does not "remove" the issue; the variance 

provides time to more fully study particular issues. 

In the section: States and EPA Must Address Increasing Complexities, in the second 

bullet we suggest you look into North Carolina's rotating basins program. It has been in 

existence for a long time and has made good use of linkages. 

In the section: Difficulty in Addressing Major External Backlog Causes, the last sentence 

of the fourth paragraph needs more explanation. 

The last paragraph has a discussion of effluent limitations guidelines that should be 

modified. More specificity would be helpful in explaining why there is a link between effluent 

limitations guidelines and backlog. We believe the existing discussion is inaccurate in cases 

where a permit has not yet incorporated an effluent guideline. Given the backlog may include 

permits of varying age, the discussion may include all the effluent guidelines promulgated in the 

last 15 years and would still be relevant today for any permits that have been expired because a 

new effluent guideline was issued. This is why we consider it a priority. Further, in another 

section of this report, the issue of guidelines is significantly downplayed because the number of 

guidelines being revised or developed related to point sources is very small. This can be 

misleading because some of the recent guidelines have potential for significant impact, for 

example powerplant intake structures, CAFOs, centralized waste treatment, etc. If a permit has 

been backlogged for a significant number of years, these new guidelines may not yet be reflected 

in the permit. Finally, the last sentence of this paragraph does not seem to make sense. We are 

unsure about the point you are making here because effluent limitation guidelines are 

technology-based not water quality-based. It should also be mentioned that effluent guidelines 

are one of the factors EPA is using for priority permits. 

Also, there are two places (p. 14 and p. 22) where the report speaks of the effect of 

"delayed" water quality standards. Does this mean the time lapse between the adoption of new 

or revised WQS and the implementation of new WQBELs in the permits or does it mean the 

backlog of standards submissions without EPA action (i.e., the WQS backlog)? We think it may 

be the latter based on the sentence on p. 14 ("EPA has stated that it will be working to reduce the 

water quality standards backlog that has delayed some new water quality standards"). If so, 

please edit the sentence on p. 22 as follows: "While we could not determine the current effect of 

the water quality standards backlog on the NPDES backlog..." 

67 
The section devoted to "Other Issues Also affect Backlog" seemed to restate a lot of issues 

already covered, so may not be necessary. However, under this section it should be noted that 

primarily states and authorized tribes issue WQS, and EPA approves (or disapproves) those, 

therefore the words "approval of" should be inserted into the following sentence as shown in 

bold: "Issues noted by State officials included ...awaiting approval of water quality standards..." 

We recommend the section for EPA Increasing Focus on Environmental Outcomes for 

Permit Issuance and Program Management be expanded and moved forward. It seems to be 

significantly downplayed at the end of this section. 

Chapter 3 - Current Impact of Backlog on Water Quality Appears Limited, but Can Grow 

in Importance 

We recommend changing the title of Chapter 3 to "Current Impact of Backlog on Water 

Quality May Be Limited, But Can Grow in Importance." Another option for a title may be, 

"Many Changes in Renewed Permits, For More Stringent Limits However Impact May Not Be 

Significant." In the situation where limits were tightened, the environmental impact may not be 

significant because dischargers were already meeting these limits. This is due to the fact as 

States adopt new water quality standards, TMDLs address more point sources, and effluent 

guidelines are incorporated, and the issue of current and appropriate controls based on these 

other factors increases in significance. Focusing on priority permit issuance along with a base of 

overall permit issuance rate addresses results while maintaining a check on program 

responsibilities. States are asking for a five year extension to permits if they are not priority 

permits which would require a change to the statute. The longer permit term would alleviate the 

backlog somewhat, however, the workload is more involved for the more complex permits. 

OIG's finding that facilities are discharging well below their permits is the intended result 

of the Effluent Guidelines and the Water Quality-Based Permitting programs. Permit limits to 

meet technology standards are set based on proven technologies that are generally affordable, so 

they are installed. Water quality-based limits are set to protect water quality standards. The 

water quality-based limits are meant to provide a safety range to prevent environmental harm; 

because discharges can vary throughout a day or month; and samples are not taken continuously. 

In most cases, the water quality-based limits are set based on data provided by the permittee for 

the effluent along with other data from the permittee or other sources for the receiving water. 

These data sets are usually very incomplete (do not include data for every day of discharge). 

The process for setting the limits considers the uncertainty due to the incomplete data sets and 

the variability of the discharge, and establishes a limit that will ensure water quality standards 

will be protected. Also, in the case of effluent guidelines, the process for issuing the guidelines 

is often lengthy. The extended amount of time provides industries with significant advance 

notice that new limitations will be put in place and industries often respond by installing 

technology in anticipation of the guideline. 

As numeric criteria are further reduced (e.g., for mercury and nutrients); however, it is 

likely that users will have to install additional treatment to reduce discharges. This will have a 

beneficial impact and lead to observable loadings reductions. 

68 
This section also looks heavily at permit limits and changes to limits over time, but misses 

some very important parts of the permit program universe, such as control of storm water and 

control of indirect discharges through the pretreatment program. Storm water is currently 

addressed through best management practices (BMPs), and the pretreatment program is 

administered at the local level and not reflected in PCS and discharge monitoring (DMR) data. 

The fact these are not included should be recognized in the discussion. Further, we feel that 

reframing the existing section may be helpful in making it easier to understand, and the 

reframing should use the chart in Appendix C. Overall it looks like a significant number of 

permits (86%) had some form of change. Over half added new parameters which could also be 

significant. According to the report, for records "that could be matched", 20 % of the permits 

included adjustments to existing limits. For decreases (57%), these changes may not have 

resulted in improved water quality because new levels were already being achieved. Increased 

levels would be considered significant to permittees because it reduces the potential liability 

(61%). This could be followed by factors addressing environmental significance. A discussion 

of the percentage of permits that may have included effluent guidelines could also be included. 

This overall discussion would also need to address the limitations of the analyses in more detail. 

The current report does not include some key points, for example it does not recognize that 

changes to monitoring requirements can have significant water quality impacts. Currently the 

analysis assumes that if the limits have not changed, there has been no change to the permit, and 

this may not be true. 

Specific Issues 

In the section, Impact of Delay in Reissuing Backlogged Permits Doubtful, the issue of 

"new" pollutants not previously limited seems to be given little attention. As one example of 

why "new" pollutants are important we can consider nutrients. Nutrients and the impact of 

nutrients on attainment of water quality standards is clear because large numbers of listed waters 

are impacted by nutrients. We suggest moving the paragraph that starts with "Our conclusions 

are limited to those limits we could match from a prior to current permit" to the beginning of the 

section to highlight the scope of the analysis that was undertaken here. 

There are 3 places (p. 17, p. 21, p. 22) where the report speaks of the increase in 

productivity of the WQS program or the increasing number of water quality standards. We are 

not sure what this really means. However, on page 22 there is a discussion of an increase in the 

number of standards submissions from 1996 to 2000 and revisions in human health criteria that 

would likely lead to new or revised WQS as well as discussion of "EPA's planned activities also 

indicate the potential for more water quality standards changes" and then it lists several items 

from the FY2005 Congressional Justification (i.e., focusing on reducing backlog of WQS, 

establishing highest attainable uses, and strengthening the scientific foundation). If this is what 

is meant by the discussions on p. 17 and p. 21, it would be helpful to move the discussion on 

page 22 forward in the document to provide context prior to the statements on pp.17 and 21. 

Comments/questions on "Delay in Reissuing Permits Had Uncertain Effect on 

Discharges" subsection -

The narrative mentions in passing numbers of permits with new limits (either additional limits on 

previously included parameters or for entirely new parameters) but does not at any point discuss 

69 
the potential significance of these new limits for water quality. Given that over half (up to as 

many as 90%, depending on the overlap between the 803 with additional limits and the 1,384 

with new parameters) of the 2,456 permits had such new limits, it would appear that this aspect 

is quite significant. 

By discussing only cases in which facilities were meeting revised permit limits prior to 

reissuance and cases in which facilities were violating both prior and revised limits, the narrative 

suggests that the cases in which discharges met the prior limits but not the revised limits, thus 

requiring a discharge reduction, were entirely insignificant. In fact, such cases are an important 

reason for reissuing permits on a regular basis. 

The term "record" is not clearly defined. It would be helpful to include a general 

description of the permit-pipe schedule-parameter-numerical limit hierarchy in the chapter itself. 

Additional explanation is needed for the first sentence of the last paragraph on p. 18, which 

parenthetically mentions numbers of maximum and average records, implying that there are 

records that are distinctly maximum and records that are distinctly average. 

The beginning of the DMR analysis discussion mentions 488 "identified" permits, but 

does not explain the criteria for selecting these 488 from the 2,456 discussed above. What were 

these criteria? 

The analysis looking at DMR data included 307 permits of the original 2,456 permit 

sample. While there is a tacit implication in the narrative that the observations from this sample 

apply to all backlogged permits, is there any information you could provide to apply the findings 

to remaining permits. 

The last paragraph of the subsection states, "We were unable to conduct a similar analysis 

for those 1,384 facilities where the new permit controlled a new pollutant." First, this seems to 

imply that each permit controls only one pollutant. Because this is not the case, and the permits 

for those 1,384 facilities almost certainly also contained limits for pollutants that had previously 

been controlled, why were the facilities rejected from the analysis, rather than analyzing the set 

of limits/discharges that were common between the backlogged and reissued permits? 

Can the information in Table 3.1 be broken into mutually exclusive categories as follows 

for Quantitative Maximum Limit Decreases (and, therefore, similarly for Quantitative Average 

Decreases)? 

Of the 797 limits analyzed, 

• 56 had discharges that would violate the revised limit, all of which were also violations 

of the prior limit 

• 797-178 = 619 had no discharges that would violate the revised limit 

• 178-56 = 122 had some discharges that met the prior limit but would violate the revised 

limit

If not, what are the problems with this type of break-out?

70 
Comments/Questions on Appendix C (given the link to this part of Chapter 3 we decided to 

include our comments on the appendix here) 

We feel the order in which the categories are listed could be changed to better group 

related categories; a better order may be: 

• Facilities/records with a current (major) permits and a previous backlogged permit in 

matching analysis 

• Facilities/records with a limit change or new parameters 

• Facilities with no new limit or new parameter and records with no limit changes 

• Facilities/records with a limit change 

o Facilities/records with a decreased limit 

o Facilities/records with a limit increase 

o Facilities/records with additional new limits for previously controlled pollutant 

[assuming this is a subset of records with a limit change] 

• Facilities/records with a new parameter 

• Could not be matched and were not a new parameter 

What is the overlap between the 1,384 facilities with new parameters and the 803 facilities 

with additional new limits for previously controlled pollutants? (Alternatively, how many 

facilities had any type of new limit?) 

Why do the 8,643 records with limit changes and the 7,812 records for new parameters 

not add up to the 14,146 records with a limit change or new parameter? At the record level, 

these categories would seem to be mutually exclusive because a limit is either new or changed 

not both. 

How many records have both a decreased limit and a limit increase? (since 4,549 + 5468 

> 8,643, there are apparently some) Presumably, these are cases with a decreased concentration 

and increased quantity (due to increased total flow), or vice versa (due to decreased total flow). 

How many are in each of these two categories? 

Are the 34,930 records listed as having no limit change identical in the prior and reissued 

permits, or does this number include the 12,926 records that were not matched and not a new 

parameter and/or the 9,061 records with changes in units? (How many records in reissued 

permits were identical to the corresponding records in prior permits?) 

In the section, Backlogged Permits Have Not Been a Major Cause of Impairment, the first 

paragraph seems to have some contradictory ideas. In one sentence, it is noted that "based on 

our review, the backlog has played only a minor role in preventing impaired waters from 

meeting their designated uses." Then in a later sentence, it is noted, "overall, we cannot 

precisely quantify the relationship of backlogged permits to impaired waters due to several 

methodological issues including." We suggest that the two sentences be combined to say that 

directly linking backlogged permits to impairments is not possible for the following reasons: 

71 
Please list methodological issues in Page 20 of report and also add: 

Impairments may be caused by a combination of sources and the relative loadings from 

these sources. These include permutations involving a single point source discharger, multiple 

point source dischargers, and non-point sources. To add to this, each type of source may 

contribute different loadings for each impairment scenario. In addition, the complexities of the 

assimilative capacity of the water body, pollutant synergies, and other factors make it very 

difficult to make direct linkages to the backlog. Therefore, keeping backlog rates as low as 

possible is desirable even when direct and compelling evidence is not available. 

Later in this same section, point sources are deemed to not be responsible for the majority 

of waters identified as impaired. This is not a factual statement that can be made until the 

TMDLs are complete for those that have a point source in them. It is true that a direct cause 

effect relationship cannot be established; ten percent are designated as "impaired solely due to 

point sources," and 50 percent are impaired "due to a combination of point and nonpoint 

sources." Thus the data indicate point sources contribute to 60 percent of the impaired waters. 

Further, a citation for these data needs to be provided and we recommend noting that the values 

presented are rough estimates (given the rough estimate we also recommend rounding the values 

in parentheses). 

The next paragraph in this section states that the results are heavily impacted by the 

"approach used and the assumption employed," but does not provide any methodology that 

describes approaches or assumptions. Therefore, it is not possible to determine the basis for 

these results. Also, the paragraph ends by stating, "Moreover, an existing approved WLA is also 

necessary for reissuance of the backlogged permit to directly address the impaired waters." 

Permits are often issued prior to the development of a TMDL; please see 40 CFR 122.44(d) that 

deals with water quality -based permits and development of permit limits. Also, the 1991 

Technical Support Document for Water Quality-based Toxics Control for detailed discussion of 

process for developing limitations. We provide similar comments on this issue in our comments 

on chapter 4. 

For table 3.2, it would be helpful to have an explanation why OW data and OECA data 

are compared for different periods of time. 

Under the section dealing with Environmental Significance, specifically dealing with 

Watershed-based Permitting and Trading, we feel more explanation is needed for the sentence, 

"Delay in incorporating these new limits may result in delay in seeing environmental benefits 

from these programs." Also, in this same paragraph, we believe clarification of the last sentence 

is necessary, perhaps to read "not being addressed in a particular rotating basin permitting 

cycle"? 

72 
Chapter 4 - GPRA Backlog Reporting Provides Inadequate Measure of Environmental 

Results 

We suggest changing the above title to "GPRA Backlog Reporting Needs to Be 

Supplemented with Environmental Results Measures." 

Progress Shown by EPA's Backlog Measure Unreliable 

We suggest that this title be changed to "EPA's Backlog Measure Considered in the 

Context of Backlog Definition Changes" 

We have always explained the reasons for the changes (administrative) in our Annual 

Reports. We will, however, make adjustments to performance measures and improve 

explanations for changes. 

Because the backlog measure is an important measure of program activity, many 

permitting authorities had varying opinions on possible definitions when tracking first began. 

EPA has made some changes to the definitions after considering factors that were not evident 

when tracking first began. Data cleanup, factoring in permit applications, and other elements 

have steadily improved the reliability of the backlog measure. 

Also, we suggest that the report consider that backlog reduction for a permitting authority 

has entailed: 

• Issuing new permits (including ones in new program areas) 

• Issuing permits that are expiring and adding new requirements 

• Issuing permits that are backlogged and integrating new requirements 

Thus, backlog reduction involves the combination of keeping up with the existing permit 

issuance workload, new universes (e.g., CAFOs, Storm Water), while issuing backlogged 

permits. The fact that many permitting authorities have been able to improve their record in the 

face of declining resources should not be characterized as being overstated. 

Accordingly, we suggest that the "measure initially overstated the actual magnitude of the 

original backlog and now overstates the magnitude of improvements" should be revised to 

include thoughts concerning the fact that issuance continued as the universe of permits expanded 

and work was underway to significantly clean up the database. While the measure has expanded 

the universe of permits to better represent the actual universe and EPA acknowledges these 

changes in FMFIA, it did not recalculate the base. It should also be recognized that many 

permitting authorities have improved permit issuance in the face of declining resources, 

additional programs coming online, and other competing interests." 

We also request the following sentence "However, a significant portion of the backlog 

reduction from minors and some portions for majors reported by EPA came from administrative 

changes rather than dramatically increased efficiency" be replaced with..."Backlog 

improvements have resulted from a combination of administrative changes (e.g., data cleanup, 

73 
changes to definitions) and increased permit issuance rates. The cleanup of databases and 

definitions that reflect the permit issuance work load are important considerations when 

evaluating backlog improvements." We should recognize program integrity as well as 

environmental significance as goals. 

Significant Portion of Improvement Due to Definition Changes 

The most significant improvement involves the change in the definition of backlog to 

include facilities covered by individual and non-storm water permits. Other factors cited 

cannot be considered significant. We suggest including the discussion of this section within the 

context of the section above. 

In anticipation of the implementation of ICIS-NPDES, EPA is in the process of revising 

the existing PCS Policy, which establishes mandatory data elements. The revised Policy will 

require permit event data to be recorded for all facilities. 

The GPRA and OWM baselines may not be consistent because they are from different 

time frames. Also, we now use a baseline (FY 2005 Annual Report) based on the 2002 data, 

which includes both individual and general permittees. We will also improve the explanations 

for the FY 2006 Annual Report and refine the baselines. 

We request that the report delete the analysis and the Table 4.2 from the report. 

In FY 1998, the OIG first identified the NPDES permit backlog as a significant 

management problem in its Audit Report "Region 10s National Pollutant Discharge Elimination 

System Permit Program." 

At that time, the NPDES inventory and the permit backlog were not systematically 

tracked nor was there consensus regarding definitions for backlog. Further, there was no clear 

guidance or existing benchmarks to determine an "acceptable" rate of backlog. 

Initially, the Permit Compliance System indicated that there were about 71,000 facilities 

with individual permits. EPA recognized that permitting authorities may have also failed to 

update PCS, leaving many facilities that were inactive or out-of-business to appear as active 

entities. At that time, there was no way of knowing which facilities among the 71,000 were 

inactive (they appeared as legitimate facilities). Also, please note that PCS has anomalies where 

inactivated facilities are only temporarily in a non-discharge status and other facilities become 

covered by general permits. ICIS will allow for linkages to be drawn to improve our ability to 

report 

When the backlog tracking began, EPA counted all facilities covered by individual 

permits showing up as active in PCS as part of the backlog because there was no other 

alternative. This definition has not changed; however, this is a program management issue that 

needs to be addressed by the permitting authorities. We believe there are still some permanently 

inactive facilities that have not been updated in PCS. 

74 
Raising awareness of the implication of "bad inventories" will prevent reoccurrence of the 

1998 situation when it was impossible to obtain reliable inventories. We continue to allocate 

funds to encourage permitting authorities to clean up data in PCS. 

As an example, an excerpt from a PCS data entry agreement for the State of Pennsylvania 

and EPA Region 3 now includes the following: 

"Cooperate in updating and maintaining permit tracking for all active facilities that have 

been identified by EPA as part of the current permit backlog and making facilities that no longer 

discharge inactive." 

We believe that our approach has been reasonable for managing the backlog data process. 

We suggest incorporating our observations into this section. 

Change in the backlog data-entry time lag from 45-days to 180 days 

As noted above, there was no consensual definition for the backlog when the project first 

began. Initially, EPA contemplated considering a permit as backlogged if the permit expiration 

date was expired at the time of the PCS end-of-month download. EPA understood that there is 

an acceptable data entry delay following the physical issuance of the permit. In general, PCS 

data entry arrangements between Regions and States allow between 5 and 30 days for data entry 

depending on data element type. Thus, the original 45-day assumption addressed data entry lag 

considerations. 

In January of 2002, EPA chose to increase the lag-time to 180-days. EPA believed that 

this lag-time allowed for consideration of factors beyond the data-entry lag-time to include: 

• Allowance for incomplete applications that extended permit issuance time frames; 

• Draft permits requiring revisions as a result of public comments; 

• Other reasons that extend the permit issuance process. 

The rationale for this increase is presented in a memorandum from Michael Cook, OWM 

Director. The memorandum focused on targeting permits languishing in backlog as opposed to 

those that have been delayed a few weeks or months due to administrative hurdles. The 

allowance for the six-month backlog accomplished this. We suggest you include this 

information in the report. 

At the same time of this memorandum, OWM was already beginning to steer towards an 

approach that identified high-and low-priority permits. OWM recognized early on that 

inventories of the backlog, while important, may not necessarily correlate with environmental 

improvements. This effort has led to the priority permit approach now in place as part of PER. 

75 
Oversight Improvements Prompted Changes in Reported Backlog 

Over the course of backlog tracking, we have adjusted inventories for two States (e.g., 

New Jersey, Minnesota). These adjustments were possible through our consistent reporting of 

the backlog data that we believe encourage States and Regions to refine the numbers. 

Backlog Measure Does Not Reflect Environmental Outcome 

EPA has now implemented a prioritization scheme designed to link permits with 

environmental outcome. 

Specific Issues 

In the first section, under the second bullet, it states "by March 2004 there were only 

about 450 more individual minors than in 1998, while the individual minors universe decreased 

by about 22,500." Looking at the data in appendix E, it seems that the word "current" was left 

out of the first clause, which should read, "by March 2004 there were only about 450 more 

current individual minors than in 1998." 

The approach used by New York DEC is highlighted. Please note that this is being 

resolved through discussions between the state and EPA Region 2. We have attached a letter 

from Region 2 to the State that describes what is being done. We believe this section should be 

removed and replaced with EPA cannot recalculate the backlog because these permits are no 

longer expired but should work with New York to assure appropriate modifications are made and 

state clearly when discussing the backlog that New York has these modifications to accomplish. 

Under the section devoted to "Inconsistencies Make Backlog Measure Unclear," the first 

bullet deals with modifications. It is not clear what is meant by "had records with between 1 and 

7 modifications." Does this mean the permit was modified? 

The section for "Limits not updated in a 'current' permit" includes the same mistake made 

earlier concerning TMDLs and NPDES permit limits. TMDL WLAs are not needed before a 

permit limit may be developed. If they are available, they are to be considered. (See 122.44(d) 

and 1991 Technical Support Document for Water Quality-based Toxics Control). 

In the section for "Backlog Measure Problems Affect Other Water Program Measures" -

the NPDES permit backlog doesn't have a direct impact on the WQS program, but it can have an 

impact on the implementation of the WQS program. Therefore, we would edit the following 

sentences as shown in bold: "Outcome-related measures for these programs assume or require 

implementation through a NPDES permit and compliance with the limits. Therefore, problems 

with the NPDES permit program, including the backlog, can have an adverse effect on the 

implementation of those other programs." 

76 
Recommendations: 

In general, we feel many of these can be combined and some dropped because they refer 

to things that the program is currently doing. 

5-1 Evaluate the effect that "feeder" programs - such as water quality standards, effluent 

guidelines, and TMDLs - have on NPDES permit limits and discharges, and take whatever steps 

feasible to better integrate the various programs in prioritizing permits for reissuance to 

ultimately achieve surface water quality improvement. 

This should be deleted. We are addressing this as part of the Priority Permits Strategy. 

We state that short-term delays in issuance are allowed and will not be counted in the backlog in 

connection with a watershed approach 

5-2 Determine whether recently developed management reports provide adequate oversight 

information through the measures by determining which management questions are answered for 

the NPDES program to better facilitate management decisions in relation to the program and 

surface water quality in general. 

This was the intent with PER, therefore, we suggest combining with the evaluation in #10. 

5-3 Determine where EPA data systems (such as PCS) do not support the measures needed to 

evaluate NPDES program performance and develop a corrective actions plan to address the 

measures or data availability. 

Because we have revised ICIS and Ask WATERS to address our needs, the issue that 

remains is data quality and data input. We suggest this be reworded to focus on this. If you need 

confirmation of specific items please let us know. 

5-4 Manage and report GPRA information on progress addressing the NPDES backlog and 

issuing permits from baselines consistent with the current backlog measure baselines (and data), 

as well as internal management baselines. In addition, clarify in reporting where measures have 

changed across reported years, and what the measure describes in terms of program performance 

and goals. EPA should also provide department-initiated modification rates information instead 

of, or in addition to, the traditional backlog measures used to track New York State's permit 

backlog. 

We recommend that the IG state that the GPRA baseline needs to reflect a PCS retrieval 

correction for a Region 6 Oil and Gas Permit that inadvertently counted pipes, inflating the 

number of permits. With the correction, the baseline is expected to decline by about 20,000 

permits. For the issues related to New York, we suggest this be reworded to capture that the 

permit modification in New York that should have been made to permit be added to the priority 

permit list for New York. 

77 
5-5 Develop and implement a plan to improve communication with States and regions on 

NPDES permitting issues; options include a periodic national NPDES conference and a 

password-protected web site for States and regions to discuss issues and have responses from 

EPA headquarters. 

Please delete. We agree and are already doing this. As discussed in our comments on 

Chapter 2, we are holding a conference in September and have had monthly conference calls all 

year. We also have specific calls on draft policy and guidance or issues with states only. 

5-6 Offer NPDES permit writer training based on a determination of State needs, potentially at a 

national meeting. 

Please delete. States request training and help determine location and frequency and we 

provide several types of training for permit writers. 

5-8 Work with Region 2 officials to complete review of whether New York's administrative 

renewal process for NPDES permits satisfies Federal requirements, especially as to use of the 

short form. If the Region does not reach a decision by June 30, 2005, Office of Water should 

conduct its own review and reach a decision, providing milestone dates for completion of 

review. 

Please delete. See response to 5-4. New York has agreed and is revising their program 

after Region 2 sent them a letter stating the need to revise the program. 

5-9 Provide a description of what management information is provided by the backlog measure 

and the supporting data, addressing State use of administrative renewals and other expedited 

reissuances, PCS data limitations, modifications, and permits that will need TMDLs to address 

water quality. 

Please delete or combine with 5-10. 

5-10 Prepare criteria for a study to evaluate the effectiveness of the prioritization approach for 

NPDES permits and the 95-percent goal of reissuance of priority permits. This study should also 

include data collection to evaluate the 5-year permit period and the appropriateness of 

distinguishing between major and minor permits for reissuance purposes. In addition, it should 

also provide feedback on the overall backlog measure in terms of what levels will be acceptable 

to EPA if there is an overall increase in backlog numbers nationally or on a State basis. 

We combined our GPRA goal of majors and minors for 2005 so this part should be 

deleted. The recommendation for an evaluation should be combined to capture whether we are 

measuring the right things to achieve the watershed objectives and do we have the right 

emphasis. This backlog measure captures program integrity rather than environmental 

significance. Because your report just looked at environmental significance, do we really need 

to look at it again? You may want to consider instead that we may want a backlog goal focused 

on 10 years for non-priority permits and retain the priority permit goal for environmental 

significance and evaluate if it is working. You may also want to include if we should consider 

78 
areas needing a TMDL or standards to be more clearly excluded from the backlog so as to not 

create a disincentive for more holistic approaches. 

5-11 Determine whether permit-related loadings measures should have a counterpart measure for 

backlogged permits reporting estimated delayed loadings reductions, and review loadings 

reduction models to ensure inclusion of actual permit results, including revised permit limits that 

remain the same or allow increased discharges over previous levels. 

We suggest adding to the end of this recommendation the idea "or include loadings in 

permit prioritization." 

79 
Appendix G 

Distribution 

Office of the Administrator 

Assistant Administrator, Office of Water 

Director, Office of Wastewater Management 

Audit Liaison, Office of Water 

Assistant Administrator, Office of Enforcement and Compliance Assurance 

Agency Followup Official (the CFO) 

Agency Followup Coordinator 

General Counsel 

Associate Administrator for Congressional and Intergovernmental Relations 

Associate Administrator for Public Affairs 

Inspector General 

80