In 1990, the U.S. Environmental Protection Agency (EPA) developed Phase I of the National Pollutant Discharge Elimination System (NPDES) in response to the 1987 Amendments to the Clean Water Act. Phase I regulations address stormwater runoff in medium and large communities, identified 11 industrial categories required to obtain permits (with some exemptions) and addressed statewide land disturbance on five acres or greater. EPA published the national Phase II Stormwater Rule in the Federal Register Dec. 8, 1999. Phase II regulations expanded the program to include smaller communities covered under municipal stormwater and land disturbance on one acre or greater. Since March 10, 2003, municipally operated industries exempted by the Intermodal Surface Transportation Efficiency Act of 1991 were required to obtain permit coverage. Provisions within the Act temporarily delayed the deadline for Phase I sources (industrial activities with the exception of power plants, airports and uncontrolled sanitary landfills) operated by municipalities with populations of less than 100,000 people to obtain an NPDES stormwater discharge permit to allow additional time to comply with requirements.

EPA delegated authority for the NPDES permitting program to the Missouri Department of Natural Resources. Under this authority, Missouri published its own stormwater regulations (10 CSR 20-6.200) in 1992. The Standard Industrial Classification (SIC) system describes 11 industrial categories, covering 30 sectors of activity, that are required to obtain stormwater discharge permits. Recently a more detailed classification system, the North American Industry Classification System, was established. Facilities review either system to choose one code based on its main type of activity or income source. If a facility has all industrial activities not exposed to stormwater, they may request a no exposure certification instead of a permit.

The department issues permits for discharging regulated stormwater. Most of these permits are written to be site-specific, issued to that one location to reflect the unique nature of the stormwater or receiving water. These permits are normally effective for five years. As a permit nears its expiration, it is redrafted, modified if needed and made available for public review and comment for 30 days on the departments Water Public Notices webpage. After the public comment period ends, the department reviews the comments. The permit is then either issued with needed changes or modified and put on public notice again to resolve any concerns.

Applications in Process

Information about permit applications in process is available in the departments' the Missouri Clean Water Information Systems (MoCWIS) application. The Applications in Process Search provides a list of water pollution permit applications received by the department. An application is considered ‘In Process’ from the date it is received until it is closed. An application is closed when the permit is issued, the application is denied or the application is withdrawn by the applicant.

Master General Permits

Master general permits, as opposed to site-specific permits, are issued to multiple locations where activities are similar enough to be covered by a single set of requirements. For stormwater discharges, these permits are identified by the prefixes MO-R in the permit number. The conditions in master general permits are made available for public review and comment for 30 days before being issued to applicants. General permits for chemical manufacturing, fabricated structured metal, foundries and wood treaters are required to be made available for public review and comment before issuance to a new facility. After finalization, a general permit cannot be modified. All facilities receiving a general permit must follow the conditions contained in that general permit until it expires or until the facility obtains a site-specific permit.

Permit Effective Date Expiration Date Description Additional Documents
MO-R040000 Phase II Municipal Separate Storm Sewer Systems

SIC/ NAICS #924110

Discharges from regulated Phase II Municipal Separate Storm Sewer Systems.

For more information, visit Municipal Separate Storm Sewer Systems (MS4).

MO-R04C000 Phase II Municipal Separate Storm Sewer Systems Comprehensive

SIC/ NAICS #924110

Discharges from regulated Phase II Municipal Separate Storm Sewer Systems - comprehensive general permit.

For more information, visit Municipal Separate Storm Sewer Systems (MS4).

MO-R100000 Area-Wide Land Disturbance

Construction or land disturbance activity (e.g., clearing, grubbing, excavating, grading and other activities that result in the destruction of the root zone and/or land disturbance activity that is reasonably certain to cause pollution to waters of the state) that are performed by or under contract to a city, county or other governmental jurisdiction that has a stormwater control program for land disturbance activities that has been approved by the Missouri Department of Natural Resources.

For more information, visit Construction Land Disturbance Permits.

Form G – Application for Land Disturbance Stormwater General Permit (MOR100 And MORA) MO 780-1408
MO-R130000 Textile and Apparel/ Printing and Publishing

SIC #20xx, 22xx, 23xx, 26xx, 27xx and 5093

Stormwater discharges from production of paper and allied products, textiles and apparel products, printing and publishing operations and paper-only recycling, food and kindred products manufacturing operations.

*The department is in the process of renewing this permit. The current permit will expire Sept. 6, 2023. If this permit is issued to your facility, you must apply for renewal of your permit a minimum of 30 days before its expiration so the department can authorize your facility to continue operating in Missouri. You must complete, sign and submit Form E - Application for General Permit Under Missouri Clean Water Law, Form MO 780-0795 to the appropriate regional office.

MO-R203000 Fabricating Metal, Light Industrial

SIC #2514, 2522, 2542, 33XX, 34XX, 35XX, 36XX, 37XX and 38XX

Stormwater discharges from ferrous and nonferrous foundries, casting, extrusion, rolling, galvanizing and finishing, structural steel production, light metal fabrication and electrical equipment manufacturing.

MO-R22A000 Lumber and Wood Primary

SIC #2421-2452, 2493, 2499, 2511, 2512, 2517, 2521, 2541 and 2861. SIC #2519, 2531, 2591 and 2599 are authorized for producers of wood furniture and products only.

Stormwater discharges from primary lumber or wood product operation (establishments engaged in sawing rough lumber and timber from logs and bolts) and facilities engaged in the secondary processing and manufacturing of lumber and wood products.

MO-R22B000 Wood Treaters

SIC #2491 & 2861 (match-light charcoal only)

Stormwater discharges from facilities engaged in wood preserving/ treating operations. This permit authorizes discharges of stormwater which have not been impacted by wastewater from wood preservation chemicals or products.

MO-R23A000 Chemical Manufacturing

SIC #28XX (except 282x and 287X) and 2992

Stormwater discharges from facilities engaging in chemical manufacturing.

MO-R23D000 Plastics and Rubber Manufacturing

SIC #2821, 2822, 2823, 2824, 2531, 30xx and 5093

Stormwater discharges associated with plastics and rubber manufacturing, molding and recycling industries.

MO-R23E000 Biodiesel Manufacturing

SIC #2841, 2869 and 2899

Stormwater runoff, secondary containment, sump and oil and water separator discharges from biodiesel manufacturing and associated facilities.

MO-R240000 Agrichemical Facilities

SIC #2873, 2874, 2875 and 2879

Facilities manufacturing, for wholesale or retail: fertilizers, pesticides and other agricultural chemicals as their primary business. 

MO-R60A000 Motor Vehicle Salvage

SIC #5015 and 5093

Stormwater runoff from motor vehicle salvage yards and scrap metal recycling operations.

MO-R80C000 Motor Freight Transportation

SIC #373X, 40XX, 41XX, 42XX, 4311 and 44XX

Firms engaged in motor freight, watercraft transportation, motorized vehicle maintenance and repair, warehousing activities, railways and U.S. Postal Service maintenance facilities.

Form E Application
MO-R80F000 Airports


Stormwater discharges from air transportation facilities that use de-icers or conduct uncovered vehicle or aircraft maintenance, washing or fueling.


MO-R80H000 Solid Waste Transfer

SIC #4953 and 5093

Stormwater discharges from solid waste transfer stations and solid waste recovery facilities.

MO-RA00000 Construction or Land Disturbance

Construction or land disturbance activity (e.g., clearing, grubbing, excavating, grading and other activities that result in the destruction of the root zone or land disturbance activity that is reasonably certain to cause pollution to waters of the state).

Currently, ePermitting must be used to apply for and receive this permit. For more information, visit Construction Land Disturbance Permits.


Stormwater Pollution Prevention Plans (SWPPPs)

More information:


Precipitation falls on impervious surfaces, such as streets and parking lots, drains to storm sewers and eventually flows to lakes and rivers. Pollutants, such as sediment and chemicals, are carried with the runoff water. As impervious surfaces increase, more water flows off of these surfaces and is delivered faster to receiving waters. Minimizing the mobilization of this material and its impact is the goal of good stormwater runoff management. Using best management practices, such as good housekeeping and in-the-ground structures, can help protect water quality.

No Exposure Certification

A condition of no exposure exists at an industrial facility when all industrial materials and activities are protected by a storm-resistant shelter to prevent exposure to rain, snow, snowmelt and runoff. Industrial materials or activities include, but are not limited to, material handling equipment or activities, industrial machinery, raw materials, intermediate products, by-products, final products or waste (including recyclable) products. Material handling activities include the storage, loading and unloading, transportation or conveyance of any raw material, intermediate product, final product or waste product.

A storm-resistant shelter is not required for the following industrial materials and activities:

  • Storage of drums, barrels, tanks and similar containers that are tightly sealed, provided those containers are not deteriorated and do not leak. “Sealed” means banded or otherwise secured and without operational taps or valves.
  • Adequately maintained vehicles used in material handling
  • Final products, other than products that would be mobilized in stormwater discharges (e.g., rock salt)

For guidance on no exposure certifications as well as a fillable form, please see below: