The National Pollutant Discharge Elimination System (NPDES), has achieved significant reductions in pollutant discharges since it was established by the Federal Water Pollution Control Act amendments of 1972.

Stormwater Management - Permitting Statistics "25 years ago, only a third of the nation's waters were safe for fishing and swimming. Wetland losses were estimated at 460 thousand acres annually. Agricultural runoff resulted in the erosion of 2.25 billion tons of soil and the deposit of large amounts of phosphorus and nitrogen into many waters.

"Over the last 25 years, the quality of rivers, lakes, and bays has improved dramatically as a result of the cooperative efforts by federal, state, tribal, and local governments and communities to implement the public health and pollution control programs. Today, two-thirds of the nation's surveyed waters are safe for fishing and swimming. Wetland losses are estimated at 70 to 90 thousand acres annually. The amount of soil lost due to agricultural run-off has been reduced by one billion tons annually." - U.S. Environmental Protection Agency (EPAOffice of Wastewater Management - Water Permitting 


What does this have to do with Flagstaff? Polluted stormwater runoff is often transported in Municipal Separate Storm Sewer Systems (MS4's) and can be discharged into local drainages without treatment. We are required to comply with the NPDES Phase II program for reducing pollution in our waterways. The EPA has granted primacy for implementing this program to the Arizona Department of Environmental Quality (ADEQ). The City of Flagstaff is currently covered under the State of Arizona General Permit number AZG2002-002.

Stormwater Phase II Rule

The EPA's Stormwater Program establishes an MS4's Stormwater Management Program that is intended to improve the nation's waterways by reducing the quantity of pollutants that stormwater picks up and carries into storm sewer systems during storms.

Contact Information

For more information on the City of Flagstaff NPDES involvement or stormwater permit contact Jolene Montoya by email or by telephone at 928-213-2117.

Small Municipal Separate Storm Sewer System General Permit

ADEQ recently issued a new small Municipal Separate Storm Sewer System (MS4) permit, effective October 31, 2022. View the new Stormwater Management Plan.

This permit is for certain public entities that operate municipal separate storm sewer systems. The permit authorizes the discharge of stormwater to U.S. waters from Small MS4s, which may include a city, town or county located fully or partially within an urbanized area as determined by the latest Decennial Census by the Bureau of Census; state, federal and other publicly-owned properties that discharge stormwater; and other areas designated by ADEQ. The permit requires the development of a stormwater management program. The permittees are required to follow six minimum control measures that must be built into their program including: Public Education and Outreach; Public Involvement and Participation; Illicit Discharge Detection and Elimination (IDDE) Program; Construction Site Stormwater Runoff Control; Post-Construction Stormwater Management; and Pollution Prevention and Good Housekeeping.

Coverage Request

The City of Flagstaff requested coverage under the 2016 MS4 by submitting a Notice of Intent (NOI) to ADEQ. ADEQ posted a public notice and proposes to issue Water Quality (AZPDES) Small MS4 General Permit (AZG2016-002) coverage to the City of Flagstaff. The City of Flagstaff is subject to provisions of the Federal Clean Water Act and the requirements of the Arizona Pollutant Discharge Elimination System (AZPDES) program, pursuant to Arizona Revised Statutes (A.R.S) Title 49, Chapter 2, Article 3.1, and Arizona Administrative Code (A.A.C.) Title 18, Article 9.

The City of Flagstaff encourages residents to view the small MS4 general permit and the NOI. Public comments are due to ADEQ by Email or mail (must be postmarked or received) by May 20, 2017. A link to the public notice on ADEQ's webpage is General Permit Coverage.

Links to Small MS4 Documents

Small MS4 General Permit (PDF)

Small MS4 Fact Sheet (PDF)

Original Published Public Notice (PDF)


Small MS4 Annual Report, ADEQ, November 29, 2021 - June 30, 2022 (PDF)


Small MS4 Annual Report, ADEQ, July 1, 2020 - June 30, 2021 (PDF)


Small MS4 Annual Report, ADEQ, July 1, 2019 - June 30, 2020 (PDF)


Small MS4 Annual Report, ADEQ, July 1, 2018 - June 30, 2019 (PDF)