Office of Inspector General
Audit Report
WATER
Kansas National Pollutant Discharge
Elimination System Program
Report No. E1HWF7-07-0022-8100089
March 31,1998

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Inspector General Division
Conducting the Audit:
Region Covered:
Central Audit Division
Kansas City, Kansas
Region 7
Program Office Involved:
Water, Wetlands, and Pesticides Division

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March 31, 1998
MEMORANDUM
SUBJECT: Kansas National Pollutant Discharge Elimination System Program
Audit Report E1HWF7-07-0022-8100089
FROM: Bennie S. Salem
Divisional Inspector General
TO:	Dennis Grams
Regional Administrator
Region 7
We have completed our audit of Kansas' National Pollutant Discharge Elimination System
Program. This report includes recommendations that Region 7 direct Kansas to establish and
implement an action plan for eliminating the backlog of expired National Pollutant Discharge
Elimination System permits. Region 7 recently notified Kansas of the Region's approval (and
disapproval of specific provisions) of the Kansas 1994 water quality standards and began
discussions with Kansas to address the recommendations within the fiscal 1999 program grant
process.
Action Required
In accordance with Environmental Protection Agency (EPA) Order 2750, you, as the
action official, are required to provide this office a written response to the audit report within 90
days of the final audit report date. For corrective actions planned, but not completed by the
response date, reference to specific milestone dates will assist in deciding whether to close this
report.
We appreciate the cooperation your staff provided throughout the audit. We especially
appreciate the program staffs assistance and timely response during the audit. The staff exhibited
a genuine interest in working with us to improve the water quality program. The staff recognized
from the beginning that this audit would provide the basis for similar audits of other states, and
worked closely with us to ensure we had a comprehensive understanding of Region 7's water
quality program. The staffs efforts helped add value to this audit and to our planned national
program audits.

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This audit report contains findings that the Office of Inspector General (OIG) has
identified and corrective actions OIG recommends. This audit report represents the opinion of
OIG, and the findings in this audit report do not necessarily represent the final EPA position.
Final determinations on matters in this audit report will be made by EPA managers in accordance
with established EPA audit resolution procedures.
We have no objections to the release of this report to the public.
If you have any questions, please call me at 551-7831 or Connie Walton, Audit Manager,
at 551-7007. Please refer to report number E1HWF7-07-0022-8100089 on any correspondence.

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Kansas National Pollutant Discharge
TABLE OF CONTENTS
PURPOSE	 1
BACKGROUND 	 1
SCOPE AND METHODOLOGY 	 3
PRIOR AUDIT COVERAGE 	4
RESULTS IN BRIEF 	4
TIMELY ISSUANCE OF PERMITS 	4
OVERSIGHT OF KANSAS PERMITS PROGRAM 	 8
OPPORTUNITY FOR ADDITIONAL ENVIRONMENTAL DATA 	 9
RECOMMENDATIONS 	 9
EXHIBIT
1 - SCOPE AND METHODOLOGY 	11
APPENDICES
I	- EPA RESPONSE 	14
II	- KANSAS RESPONSE 	17
III	- DISTRIBUTION 	22
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Kansas National Pollutant Discharge
Eliminatioi^^tenn*rogran^^^^^
PURPOSE	The Clean Water Act required the Environmental Protection
Agency (EPA) to control point sources of water pollution
through the National Pollution Discharge Elimination
System, hereafter referred to as the "permits" program. The
permits program is EPA's primary regulatory tool for
controlling pollutant discharges into surface waters. We
selected the Kansas permits program for audit because
Office of Water personnel suggested several states,
including Kansas, where audits could identify best practices
and needed improvements in states' permits programs. Our
specific objectives were to determine if:
Kansas implemented procedures to ensure
complete and timely permits were issued for
dischargers;
Kansas restricted waste dischargers based on
effluent limitations and established
monitoring requirements for each pollutant;
Kansas monitored permit conditions,
including effluent limitations and compliance
schedules;
Kansas permitted stormwater, combined
sewer, sludge, and pretreatment program
activities; and
Region 7 monitored Kansas' implementation
of the permits program and established
controls to ensure that water quality goals
are met.
BACKGROUND	The Federal Water Pollution Control Act amendments of
1972 included the permits program as the centerpiece of the
national water pollution control efforts. Congress
reauthorized and renamed the Act the Clean Water Act in
1977 and amended it in 1987. Permits limit the pollutants
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Kansas National Pollutant Discharge
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that a facility may discharge into United States waters
through a specific point, such as a pipe. The Code of
Federal Regulations (CFR) Title 40, Parts 122 to 133 and
Parts 401 to 503 contain EPA regulations for implementing
and administering the permits program.
EPA classifies permitted facilities primarily as municipal and
non-municipal. Municipal facilities typically treat municipal
sewage or industrial wastes to acceptable limits and
discharge the treated wastes into United States waters.
Non-municipal facilities include industrial facilities and all
other facilities that discharge pollutants directly into United
States waters rather than through municipal facilities.
EPA also classifies facilities as either major or minor. EPA
regulations define major municipal facilities as those having
a design or actual flow of one million gallons or greater per
day. Major non-municipal facilities are determined based on
specific ratings criteria developed by EPA and states.
Kansas had 56 major and 776 minor facilities in August
1997. Of the 56 major facilities, 40 were municipal and 16
were non-municipal.
The permits program originally focused on the municipal
and non-municipal facilities. As the program matured and
municipal and non-municipal facilities' discharges were
permitted, the focus of the permits program expanded to
regulate other pollution sources. These newer programs
include pretreatment, stormwater, combined sewer, and
sludge programs.
The pretreatment program regulates wastewater from
industrial facilities that discharge to municipal facilities and
is primarily implemented directly by the municipal facility
receiving industrial wastes. The stormwater program
regulates large volumes of water that can result from
surface runoff, street washing, rain, and snowmelt that drain
to receiving waters. The combined sewer program was
designed to regulate untreated overflows into receiving
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Kansas National Pollutant Discharge
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waters from municipalities with combined sewer systems.
The sludge program regulates the use and disposal of the
semisolid residue from municipal facilities.
In addition to pollutant discharge limits, permits contain
requirements to monitor and report on pollutant discharges.
States enter major facilities' discharge monitoring data into
the Permit Compliance System. The Permit Compliance
System is a centralized repository of information used to
determine reductions in pollutants discharged to the United
States waters.
Region 7 delegated its authority to administer the Kansas
permits program to the Kansas Department of Health and
Environment. The Kansas Department of Health and
Environment is responsible for protecting and maintaining
Kansas' water quality. The Division of Environment within
the Kansas Department of Health and Environment is
responsible for implementing Kansas' permits program. In
fiscal 1998, EPA provided $850,000 in grants to the Kansas
Department of Health and Environment for Kansas' water
quality program which includes the permits program.
SCOPE AND	We performed our audit in accordance with Government
METHODOLOGY	Auditing Standards (1994 revision) issued by the
Comptroller General of the United States as they apply to
program audits. Our review included tests of the program
records and other auditing procedures we considered
necessary. We conducted our fieldwork from June 1997
through January 1998. We performed our fieldwork at
Region 7 in Kansas City, Kansas, and at Kansas Department
of Health and Environment in Topeka, Kansas.
See Exhibit 1 for scope and methodology details.
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Kansas National Pollutant Discharge
Eliminatioi^^tenn*rogran^^^^^
PRIOR AUDIT	The Office of Inspector General issued an audit report
COVERAGE	entitled Region 7's Efforts to Address Water Pollution
From Livestock Waste (E1HWF6-07-0017-6100312),dated
September 30, 1996, and reported that a more structured
approach was needed to address livestock waste. The
United States General Accounting Office has not issued
recent reports directly related to the Kansas permits
program.
RESULTS IN BRIEF	When Kansas issued permits, it established permit limits and
monitoring requirements, and inspected permittee
operations in accordance with EPA regulations. Further,
Kansas permitted stormwater, combined sewer, and
pretreatment program activities in accordance with EPA
regulations. However, Kansas did not reissue expired
permits timely. Kansas' failure to submit expired permits
for Region 7 review limited the Region's options to ensure
Kansas' permits program controlled pollutant discharges
into Kansas' waters. As a result, the permittees were
allowed to discharge pollutants at levels that could
adversely affect aquatic life and human health.
TIMELY ISSUANCE	Kansas did not reissue 22 percent of its expired permits in
OF PERMITS	the required timeframe. Federal regulations require the
periodic review of permits to ensure that changed
conditions and advancements in science are considered in
establishing permit limits. As of August 1997, Kansas had
832 permits, of which 182 were expired for periods up to 6
years. Kansas officials said they had not reissued these
permits due to their change in permitting approach, state
legislative mandates, and Region 7's failure to approve
Kansas' 1994 water quality standards. As these facilities
continue to operate under their expired permits, they may
discharge pollutants at levels that could adversely affect
aquatic life and human health.
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Kansas National Pollutant Discharge
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CFR part 122.46, Duration of permits, requires that the
duration of permits not exceed 5 years. CFR part 122.6,
Continuation of expiring permit, allows an expired permit
to remain in effect until a new permit is issued.
States are required to develop water quality standards that
serve as the regulatory basis for pollutant discharge limits in
the permits program. Section 303 of the Clean Water Act,
Water Quality Standards and Implementation Plans,
requires states to review their water quality standards once
every 3 years and obtain EPA approval for the standards.
EPA is required to promulgate water quality standards for
the state if EPA disapproves a state's water quality
standards. CFR part 131.21, EPA review and approval of
water quality standards, provides that a state's water
quality standards remain in effect unless EPA promulgates
standards for the state.
The status of Kansas permits, as of August 1997, by major
and minor facilities are shown in Table 1.
Table 1: Expired Permits
Type of
Facility
Number of
Permits
Number of
Expired
Permits
Percent
Expired
Major
56
26
46
Minor
776
156
20
TOTAL
832
182
22
We analyzed the backlog of the 26 expired major permits
and found 2 were subsequently issued. Of the remaining 24
permits, 6 were attributed to Kansas' change in permitting
approach, 17 to changes in the ammonia water quality
standard, and 1 to changes in the arsenic water quality
standard.
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Kansas National Pollutant Discharge
Change in Permitting	In 1994, Kansas changed its permitting approach to issue all
Approach	permits in a geographical location, or basin, at the same
time. This approach allows Kansas to more effectively
develop permit limits for all dischargers in the same basin,
using water quality data from the same point in time. Six of
the major expired permits were located in the Kansas Lower
Republican Basin. This basin is Kansas' current priority for
implementing the new permitting approach. Thus, we
believe it is reasonable that the permits were temporarily
allowed to expire to switch all permits in the Kansas Lower
Republican Basin to the same permit cycle.
Change in Ammonia Water	Kansas did not issue 17 major permits pending resolution of
Quality Standard	differences between Kansas and Region 7 over ammonia
water quality standards. Kansas adopted more restrictive
ammonia water quality criteria in 1994. However, Kansas
officials said they could not issue the permits using the more
restrictive 1994 ammonia limits because Region 7 had not
approved Kansas' 1994 water quality standards. In 1994,
Kansas adopted an ammonia water quality standard that was
compatible with EPA's 1985 ammonia guidance. Region 7
was supportive of Kansas' 1994 ammonia standard and
complimented the State on its revision. However, Region 7
did not formally approve Kansas' 1994 water quality
standards due to concerns with pollutants other than
ammonia.
Permittee complaints and EPA's lack of formal response to
the 1994 Kansas water quality standards led to Kansas
House Bill 2368, dated May 1, 1997. The House Bill
provided permittees their choice of ammonia permit limits
based on Kansas' 1994 standard or interim limits based on
the less restrictive 1987 standard, pending a special
commission review of Kansas surface water quality
standards. The House Bill cited uncertainty over the science
used to develop Kansas' 1994 ammonia standard and the
social and economic costs to meet the 1994 standard.
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Kansas National Pollutant Discharge
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The uncertainty over the science rose from the types of
aquatic life used in EPA's testing. EPA acknowledged that
the science that supported its 1985 ammonia guidance was
based on aquatic life that may not be indigenous to all
states. However, Kansas developed its 1994 ammonia
standards based on its own studies using aquatic life
indigenous to the State.
The House Bill also cited Kansas' concern over the social
and economic cost to meet the 1994 ammonia standard.
Kansas officials identified 5 of the 17 facilities that would
need plant upgrades to meet the 1994 ammonia standard.
Kansas officials thought the remaining 12 major facilities
would not require upgrades; however, they believed the
permittees would not agree to ammonia permit limits. As a
result, Kansas did not issue the 17 permits and stopped the
permits issuance process prior to submitting the permits for
public comment and Region 7 review. These permittees
continue to operate under their less restrictive expired
permits.
Kansas did issue several major facility permits that limited
ammonia based on the 1994 ammonia water quality
standard. During 1997, Kansas issued permits containing
ammonia limits based on its 1994 ammonia water quality
standard to two major municipal wastewater treatment
plants. Kansas officials said that the facilities needed to
upgrade the treatment plants for reasons other than
ammonia; however, Kansas developed the permits limits
using the 1994 ammonia standard as the basis of design for
the new treatment plant.
Change in Arsenic Water
Quality Standard
Kansas did not issue one major permit pending resolution of
differences between Kansas and Region 7 over the arsenic
water quality standards. EPA promulgated water quality
standards for Kansas in 1991 which included standards for
arsenic. Kansas did not agree with the national promulgated
arsenic standards, and adopted a less restrictive standard in
1994. Region 7 had concerns whether Kansas' 1994 arsenic
standard was protective of human health and did not
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Kansas National Pollutant Discharge
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approve the standard. Kansas and Region 7 are still in
negotiations over this water quality standard. As the new
permit had not been issued, the permittee is operating under
the expired permit, which includes arsenic limits that are not
as strict as current EPA science. As a result, this permittee
may be discharging arsenic at levels unsafe for human
health.
OVERSIGHT OF	Kansas' failure to submit expired permits for Region 7
KANSAS PERMITS	review limited the Region's oversight options to ensure that
PROGRAM	the Kansas permits program appropriately controlled
pollutant discharges in Kansas waters. As Kansas did not
submit the revised permits to Region 7, the Region could
not review and approve or comment on the permits.
CFR part 123.43 Transmission of information to EPA,
requires that states submit draft permits to EPA for review
at the same time the permit is submitted for public notice.
The regulations provide that EPA may only issue a permit in
a delegated state if objections are raised and not resolved.
Region 7's failure to approve the Kansas 1994 water quality
standards contributed to the Kansas permits backlog. The
Region recognized its need to approve state standards as a
fiscal 1997 Federal Managers' Financial Integrity Act area
of concern, and committed in its fiscal 1998/1999 regional
management agreement with Office of Water to complete
timely approval actions.
Region 7 and Kansas also recognized Kansas' permits
backlog as a concern in 1996, and established the issuance
of expired permits as a high priority in Kansas' fiscal 1997
annual work plan. The annual work plan identifies mutual
expectations as well as the State's responsibilities and
priorities for the upcoming year. However, the Region did
not exercise its option of withholding grant funds for
Kansas' failure to issue expired permits.
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Kansas National Pollutant Discharge
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OPPORTUNITY FOR	Region 7 developed a software program for Kansas that
ADDITIONAL	may be used to improve the quality of environmental data
ENVIRONMENTAL	used to measure the success of the permits program. EPA
DATA	does not require states to record minor permittee discharge
monitoring data in the Permit Compliance System as the
process is time-consuming and expensive; however, CFR
part 123.45 Noncompliance and program reporting by the
Director, does require states to report on their reviews,
compliance issues, and enforcement actions for minor
permits. Region 7 developed a software program that
electronically transfers discharge monitoring data from
Kansas' 56 major facilities to the Permit Compliance
System. Kansas could use the program to record discharge
monitoring data for its 776 minor facilities, as the program
eliminates the time and expense barriers to recording minor
permittee monitoring data.
EPA uses the discharge monitoring data as a surrogate
environmental indicator of the success of the permits
program. This environmental indicator may be significantly
misstated in Kansas as 93 percent of the permitted facilities
in Kansas are minors.
RECOMMENDATIONS	We recommend the Regional Administrator direct the
Water, Wetlands, and Pesticides Division to:
1.	Encourage Kansas to submit all expired
permits for major facilities for public
comment and Region 7 review.
2.	Direct Kansas to establish an action plan for
eliminating the backlog of expired permits.
3.	Work with Kansas to assess the effect of its
permits backlog in developing its water
quality monitoring plan.
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Kansas National Pollutant Discharge
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4.	Develop an action plan for the timely review
of and prompt action on state water quality
standards.
5.	Negotiate with Kansas to provide data on
minor dischargers in the Permit Compliance
System using the newly developed software.
AUDITEE COMMENTS	Region 7 generally agreed with the findings and
AND OIG EVALUATION	recommendations. Kansas Department of Health and
Environment agreed that the report was substantially
accurate and factual. Both Region 7 and Kansas provided
comments to clarify portions of the report, and we have
incorporated these comments and modified the report as
appropriate.
Both Region 7 and Kansas indicated that they had begun
taking corrective actions through discussion in the fiscal
1999 program grant process. Further, Region 7 notified
Kansas of the Region's approval (and disapproval of
specific provisions) of Kansas' water quality standards.
Both Region 7 and Kansas emphasized that the Results in
Brief conclusion, "... permittees were allowed to discharge
pollutants at levels that could adversely affect aquatic life
and human health" acknowledges the uncertain results of
the expired permits. However, neither Region 7 nor Kansas
was aware of any evidence of actual impacts to aquatic life
or human health from expired permits. Kansas noted that
they would act swiftly to minimize such risk if they were
aware of factual instances where human life was at imminent
risk.
Kansas felt that it would not be cost beneficial to provide
data on minor dischargers in the Permit Compliance System
using the Region 7 developed software. As EPA uses the
discharge monitoring data as a surrogate environmental
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Kansas National Pollutant Discharge
indicator of the success of the permits program, we
recommend that Kansas consider prioritizing the minor
dischargers and use the software program as they have
resources.
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Kansas National Pollutant Discharge
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Exhibit 1
SCOPE AND METHODOLOGY
We reviewed Kansas' internal controls over the permits program. We analyzed internal controls
to assure compliance with federal statutory and regulatory criteria and with the State's policies
and procedures. We determined whether Region 7's Federal Managers' Financial Integrity Act
reports disclosed any material weaknesses applicable to the audit. Our audit disclosed several
areas needing improvement that are discussed in the report.
We focused on the 832 permits Kansas issued to municipal and non-municipal facilities to limit
pollution discharges. The review did not include permits for confined animal feeding operations,
as these are zero discharging permits and were addressed in a prior audit. Further, the review did
not include Kansas supplement permits are not part of the National Pollution Discharge
Elimination System.
To determine whether Kansas procedures ensured complete and timely permits were issued and
whether permit limits were appropriately calculated and monitored, we interviewed Kansas and
Region 7 officials to obtain an understanding of their procedures for administering the permits
program. We compared permit procedures to applicable laws, regulations, and documentation
provided by Region 7 and Kansas.
We selected a judgmental sample of 10 of Kansas' 832 permits to determine if Kansas
implemented procedures to ensure complete permits were issued. The 10 permits were for major
and minor facilities located in areas of impaired water. We compared the permit information to
the requirements in CFR parts 122 to 133, and the Permit Writers Manual (EPA-833-B-96-003),
dated December 1996. We analyzed Kansas' automated permit data to evaluate the timeliness of
permits issued.
To determine whether Kansas monitored permit conditions, including effluent limitations and
compliance schedules, we reviewed Kansas' inventory of inspections and reviewed the contents of
inspection reports. We obtained Kansas' procedures for monitoring discharges and compared
monthly discharge monitoring report data with permit limits to determine if permittees complied
with effluent limits.
To determine whether Kansas effectively permitted stormwater, combined sewers, sludge, and
pretreatment, we interviewed Kansas and Region 7 personnel to determine how they ensured
programs operated in compliance with EPA regulations. For stormwater, we reviewed the basic
permit to determine if the required elements were included and if stormwater permits were issued
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Kansas National Pollutant Discharge
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for construction sites. We reviewed the three Kansas combined sewer permits to determine if the
permits included the required controls and long range plans. To evaluate the Kansas sludge
program, we reviewed three annual reports and sludge procedures for compliance with sludge
regulations. Also, we reviewed controls over the 15 approved pretreatment programs and
determined if municipal facilities' permits included pretreatment requirements.
To evaluate Region 7 monitoring of Kansas implementation of the permits program, we
interviewed Region 7 personnel to determine how they evaluated the Kansas permits program.
We reviewed management agreements to determine required performance. We reviewed Kansas
work plans to evaluate activities and performance reporting. We also reviewed correspondence
between Region 7 and Kansas to identify issues or areas of interest.
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Kansas National Pollutant Discharge
Appendix I
AUDITEE RESPONSE
TO BE ADDED.
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Kansas National Pollutant Discharge
Eliminatioi^^tenn*rogran^^^^^
Appendix III
DISTRIBUTION
Office of Inspector General
Inspector General (2410)
Deputy Assistant Inspector General for Internal Audits (2421)
Headquarters Audit Liaison (2421)
Divisional Inspectors General for Audit
EPA Headquarters Office
Assistant Administrator for Water (4101)
Agency Followup Official (2710)
Agency Followup Coordinator (3304)
Associate Administrator for Congressional and Legislative Affairs (1301)
Associate Administrator for Communications, Education, and Public Affairs (1701)
Associate Administrator for Regional Operations and State/Local Relations (1501)
Headquarters Library (3401)
EPA Region 7
Director, Water, Wetlands, and Pesticides Division
Director, Office of External Programs
Audit Followup Coordinator
Regional Offices
Regional Administrators
Kansas Division of Environment
Director
Director, Bureau of Water
Chief, Water Technical Services Section
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