United States 

Environmental Protection 

Agency 

Office of Water 

(4203) 

EPA 833-F-011

January 2000 (revised December 2005) Fact Sheet 2.9

Stormwater Phase II 

Final Rule 

Fact Sheet Series 

Overview 

1.0 – Stormwater Phase II Final 

Rule: An Overview 

Small MS4 Program 

2.0 – Small MS4 Stormwater 

Program Overview 

2.1 – Who’s Covered? Designation

and Waivers of Regulated Small 

MS4s 

2.2 – Urbanized Areas: Definition 

and Description 

Minimum Control Measures 

2.3 – Public Education and 

Outreach 

2.4 – Public Participation/ 

Involvement 

2.5 – Illicit Discharge Detection 

and Elimination 

2.6 – Construction Site Runoff 

Control 

2.7 – Post-Construction Runoff 

Control 

2.8 – Pollution Prevention/Good

Housekeeping 

2.9 – Permitting and Reporting:

The Process and Requirements 

2.10 – Federal and State-Operated

MS4s: Program Implementation 

Construction Program 

3.0 – Construction Program

Overview 

3.1 – Construction Rainfall 

Erosivity Waiver 

Industrial “No Exposure” 

4.0 – Conditional No Exposure

Exclusion for Industrial Activity 

Stormwater Phase II 

Final Rule 

Permitting and Reporting:

The Process and Requirements

The Stormwater Phase II Final Rule requires operators of certain small municipal separate storm 

sewer systems (MS4s) to obtain National Pollutant Discharge Elimination System (NPDES) 

permit coverage because their stormwater discharges are considered “point sources” of pollution. 

All point source discharges, unlike nonpoint sources such as agricultural runoff, are required 

under the Clean Water Act (CWA) to be covered by federally enforceable NPDES permits. Those 

systems already permitted under the NPDES Phase I stormwater program, even systems serving less 

than 100,000 people, are not required to be permitted under the Phase II stormwater program. 

NPDES stormwater permits are issued by an NPDES permitting authority, which may be an NPDESauthorized State or a U.S. EPA Region in non-authorized States. Issued MS4 permit conditions must 

be satisfied (i.e., development and implementation of a stormwater management program) and 

periodic reports must be submitted on the status and effectiveness of the program. 

This fact sheet explains the various permit options that are available to operators of regulated 

small MS4s and details the permit application and reporting requirements. Program requirements for 

regulated small MS4s are explained in Fact Sheets 2.0 through 2.8. 

What Permitting Options Are Available to Operators of Regulated Small 

MS4s? 

Unlike the Phase I program that primarily utilizes individual permits for medium and large MS4s, 

the Phase II approach allows operators of regulated small MS4s to choose from as many as three 

permitting options as listed below. At this time the NPDES permitting authorities have issued 

general permits for regulated small MS4s. Operators of regulated small MS4s in urbanized areas, 

whether automatically designated or designated by the permitting authority, should have submitted 

their permit applications within 90 days of permit issuance. Regulated small MS4 stormwater 

management programs should be fully developed and implemented by the end of the first permit 

term, which is typically a 5-year period. The NPDES permitting authority reserves the authority 

to determine which permitting options are available to the regulated small MS4s. Refer to specific 

NPDES permitting authority for more details about permitting options in particular states. 

‘ General Permits 

• General permits are strongly encouraged by EPA. The Phase II program has been designed 

specifically to accommodate a general permit approach. 

• General permits prescribe one set of requirements for all applicable permittees. General 

permits are drafted by the NPDES permitting authority, then published for public comment 

before being finalized and issued. 

• A Notice of Intent (NOI) serves as the application for the general permit. The permittee 

complies with the permit requirements by submitting an NOI to the NPDES permitting 

authority that describes the stormwater management plan, including best management 

practices (BMPs) and measurable goals. A Phase II permittee has the flexibility to develop 
Fact Sheet 2.9 – Permitting and Reporting: The Process and Requirements Page 2 

an individualized stormwater program that addresses 

the particular characteristics and needs of its system, 

provided the basic requirements of the general permit 

are satisfied. 

• Permittees also can choose to share responsibilities for 

meeting the Phase II program requirements. Those 

entities choosing to do so may submit jointly with the 

other municipalities or governmental entities an NOI 

that identifies who will implement which minimum 

measures within the area served by the MS4. 

• The permittee then follows the Phase II permit 

application requirements (see discussion in next 

question below). 

Minimize Duplication of Effort 

Two permitting options tailored to minimize duplication of 

effort can be incorporated into the general permit by the 

NPDES permitting authority. First, the permitting authority can 

recognize in the permit that another governmental entity is 

responsible under an NPDES permit for implementing any or 

all minimum measures. Responsibility for implementation 

of the measure(s) would rest with the other governmental 

entity, thereby relieving the permittee of its responsibility to 

implement that particular measure(s). For example, the NPDES 

permitting authority could recognize a county erosion and 

sediment control program for construction sites that was 

developed to comply with a Phase I permit. As long as the 

Phase II MS4s in the county comply with the county’s 

construction program, they would not need to develop and 

implement their own construction programs because such 

activity would already be addressed by the county. 

Second, the NPDES permitting authority can include 

conditions in a general permit that direct a permittee to follow 

the requirements of an existing qualifying local program rather 

than the requirements of a minimum measure. A qualifying 

local program is defined as a local, State or Tribal municipal 

stormwater program that imposes requirements that are 

equivalent to those of the Phase II MS4 minimum measures. 

The permittee remains responsible for the implementation of 

the minimum measure through compliance with the qualifying 

local program. 

‘ Individual Permits 

• Individual permits are required for Phase I “medium” 

and “large” MS4s, but not recommended by EPA for 

Phase II program implementation. 

• The permittee can either submit an individual 

application for coverage by the Phase II MS4 program 

(see 40 CFR §122.34) or the Phase I MS4 program 

(see 40 CFR §122.26(d)). 

• For individual coverage under Phase II, the permittee 

must follow Phase II permit application requirements 

and provide an estimate of square mileage served by 

the system and any additional information requested 

by the NPDES permitting authority. A permittee 

electing to apply for coverage under the Phase I 

program must follow the permit application 

requirements detailed at 40 CFR §122.26(d). 

• The NPDES permitting authority may allow more than 

one regulated entity to jointly apply for an individual 

permit. 

• The NPDES permitting authority could incorporate 

in the individual permit either of the two permitting 

options explained above in the Minimize Duplication 

of Effort section. 

‘ Modification of a Phase I Individual Permit – 

A Co-Permittee Option 

• The operator of a regulated small MS4 could 

participate as a limited co-permittee in a neighboring 

Phase I MS4’s stormwater management program 

by seeking a modification of the existing Phase I 

individual permit. A list of Phase I medium and large 

MS4s can be obtained from the EPA Office of 

Wastewater Management (OWM) or downloaded 

from the OWM web site. 

• The permittee must follow Phase I permit application 

requirements (with some exclusions). 

• The permittee must comply with the applicable terms 

of the Phase I individual permit rather than the 

minimum control measures in the Phase II Final Rule. 

What Does the Permit Application Require? 

Operators of regulated small MS4s are required to submit in 

their NOI or individual permit application the following 

information: 

‘ Best management practices (BMPs) are required for 

each of the six minimum control measures: 

Ø Public education and outreach on stormwater 

impacts 

Ù Public participation/involvement 

Ú Illicit discharge detection and elimination 

Û Construction site stormwater runoff control 

Ü Post-construction stormwater management in new 

development/redevelopment 

Ý Pollution prevention/good housekeeping for 

municipal operations 
Fact Sheet 2.9 – Permitting and Reporting: The Process and Requirements Page 3 

(See Fact Sheets 2.3 through 2.8 for full descriptions 

of each measure, including examples of BMPs and 

measurable goals) 

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Measurable goals for each minimum control measure 

(i.e, narrative or numeric standards used to gauge 

program effectiveness); 

Estimated months and years in which actions to 

implement each measure will be undertaken, including 

interim milestones and frequency; and 

The person or persons responsible for implementing or 

coordinating the stormwater program. 

Relying on Another Entity 

The Phase II permittee has the option of relying on other 

entities already performing one or more of the minimum control 

measures, provided that the existing control measure, 

or component thereof, is at least as stringent as the Phase II rule 

requirements. For example, a county already may have an 

illicit discharge detection and elimination program in place and 

may allow an operator of a regulated small MS4 within the 

county’s jurisdiction to rely on the county program instead of 

formulating and implementing a new program. In such a case, 

the permittee would not need to implement the particular 

measure, but would still be ultimately responsible for its 

effective implementation. For this reason, EPA recommends 

that the permittee enter into a legally binding agreement with 

the other entity. If the permittee chooses to rely on another 

entity, they must note this in their permit application and 

subsequent reports. A Phase II permittee may even rely on 

another governmental entity regulated under the NPDES 

storm water program to satisfy all of the permittee’s permit 

obligations. Should this option be chosen, the permittee must 

note this in its NOI, but does not need to file periodic reports. 

What Does the Permit Require? 

The operator of a regulated small MS4 has the flexibility 

to determine the BMPs and measurable goals, for each 

minimum control measure, that are most appropriate for the 

system. The chosen BMPs and measurable goals, submitted 

in the permit application, become the required stormwater 

management program; however, the NPDES permitting 

authority can require changes in the mix of chosen BMPs 

and measurable goals if all or some of them are found to be 

inconsistent with the provisions of the Phase II Final Rule. 

Likewise, the permittee can change its mix of BMPs if it 

determines that the program is not as effective as it could 

be Fact Sheets 2.3 through 2.8 further describe each of the 

minimum control measures, while the permit requirements 

for evaluation/assessment and recordkeeping activities are 

described in separate sections below. 

Menu of BMPs 

The BMPs for minimum measures 3 through 6 (as listed in 

the permit application requirements section, above) are not 

enforceable until the NPDES permitting authority provides a 

list, or “menu,” of BMPs to assist permittees in the design and 

implementation of their stormwater management programs. 

The NPDES permitting authority was required to provide this 

menu as an aid for those operators that are unsure of the most 

appropriate and effective BMPs to use. Since the menu was 

intended to serve as guidance only, the operators can either 

select from the menu or identify other BMPs to meet the permit 

requirements. EPA has developed a menu of BMPs that can be 

accessed at EPA’s Stormwater Web Site 

(http://www.epa.gov/npdes/stormwater). 

What Standards Apply? 

APhase II small MS4 operator is required to design a 

program that: 

‘

‘

‘

Reduces the discharge of pollutants to the “maximum 

extent practicable” (MEP); 

Protects water quality; and 

Satisfies the appropriate water quality requirements of 

the Clean Water Act. 

Compliance with the technical standard of MEP requires the 

successful implementation of approved BMPs. The Phase II 

Final Rule considers narrative effluent limitations that require 

the implementation of BMPs and the achievement of 

measurable goals as the most appropriate form of effluent 

limitations to achieve the protection of water quality, rather 

than requiring that stormwater discharges meet numeric effluent 

limitations. 

EPA issued Phase II NPDES permits consistent with its August 

1, 1996, Interim Permitting Approach policy, which calls for 

BMPs in first-round stormwater permits and expanded or better 

tailored BMPs in subsequent permits, where necessary, to 

provide for the attainment of water quality standards. In cases 

where information exists to develop more specific conditions or 

limitations to meet water quality standards, these conditions or 

limitations should be incorporated into the stormwater permit. 

Monitoring is not required under the Phase II Rule, but the 

NPDES permitting authority has the discretion to require 

monitoring if deemed necessary. 

What Evaluation/Reporting Efforts Are 

Required? 

Frequency of Reports 

Reports must be submitted annually during the first permit 

term. For subsequent permit terms, reports must be submitted 

in years 2 and 4 only, unless the NPDES permitting authority 

requests more frequent reports. 
Fact Sheet 2.9 – Permitting and Reporting: The Process and Requirements Page 4 

Required Report Content 

The reports must include the following: 

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‘

‘

‘

‘

The status of compliance with permit conditions, 

including an assessment of the appropriateness of the 

selected BMPs and progress toward achieving the 

selected measurable goals for each minimum measure; 

Results of any information collected and analyzed, 

including monitoring data, if any; 

A summary of the stormwater activities planned for the 

next reporting cycle; 

A change in any identified best management practices 

or measurable goals for any minimum measure; and 

Notice of relying on another governmental entity to 

satisfy some of the permit obligations (if applicable). 

A Change in Selected BMPs 

If, upon evaluation of the program, improved controls are 

identified as necessary, permittees should revise their mix of 

BMPs to provide for a more effective program. Such a change, 

and an explanation of the change, must be noted in a report to 

the NPDES permitting authority. 

What are the Recordkeeping Requirements? 

Records required by the NPDES permitting authority must 

be kept for at least 3 years and made accessible to the 

public at reasonable times during regular business hours. 

Records need not be submitted to the NPDES permitting 

authority unless the permittee is requested to do so. 

What Are the Deadlines for Compliance? 

As stated previously, the NPDES permitting authorities have 

issued permits for regulated small MS4s. Operators of 

regulated small MS4s in urbanized areas, whether automatically 

designated or designated by the permitting authority, should 

have submitted their permit applications within 90 days of 

permit issuance. Regulated small MS4 stormwater management 

programs should be fully developed and implemented by the 

end of the first permit term, typically a 5-year period. 

What are the Penalties for Noncompliance? 

The operator of a regulated small MS4 is required to obtain 

an NPDES permit that is federally enforceable, thus 

subjecting the permittee to potential enforcement actions and 

penalties by the NPDES permitting authority if the MS4 

operator does not fully comply with application or permit 

requirements. This federal enforceability also includes the right 

for interested parties to sue under the citizen suit provision of 

the CWA (section 505; 33 USC § 1365). 

For Additional Information 

Contacts 

L

L

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U.S. EPA Office of Wastewater Management 

http://www.epa.gov/npdes/stormwater 

Phone: 202-564-9545 

Your NPDES Permitting Authority. Most States and 

Territories are authorized to administer the NPDES 

Program, except the following, for which EPA is the 

permitting authority: 

Alaska Guam 

District of Columbia Johnston Atoll 

Idaho Midway and Wake Islands 

Massachusetts Northern Mariana Islands 

New Hampshire Puerto Rico 

New Mexico Trust Territories 

American Samoa 

A list of names and telephone numbers for each EPA 

Region and State is located at http://www.epa.gov/ 

npdes/stormwater (click on “Contacts”). 

Reference Documents 

L EPA’s Stormwater Web Site 

http://www.epa.gov/npdes/stormwater 

• Stormwater Phase II Final Rule Fact Sheet Series 

• Stormwater Phase II Final Rule (64 FR 68722) 

• National Menu of Best Management Practices for 

Stormwater Phase II 

• Measurable Goals Guidance for Phase II Small 

MS4s 

• Stormwater Case Studies 

• And many others