Permits are required to build, erect, alter, replace, operate, use or maintain existing point sources of water pollution. The majority of our permits are for discharging treated wastewater from domestic and industrial facilities. We also issue permits for land application of wastes from domestic, industrial and agricultural facilities. Our permits usually specify requirements for regular wastewater sampling at the discharge points. In the case of land application, the permit specifies the methods by which wastes are handled and disposed. Permits also specify water quality standards for any discharges.

Most of these permits are written to be site-specific, issued to that one location to reflect the unique nature of the wastewater or the 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.

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 wastewater discharges, these permits are identified by the prefix MO-G in the permit number. The conditions in master general permits are also made available for public review and comment for 30 days before being issued to applicants. General permits for airports, limestone and rock quarries, lubricant manufacturing and petroleum storage greater than 50,000 gallons 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.

Applications in Process

Information about permit applications in process is available in the departments' 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.

New Master General Permits in Development

MO-G330000 Extended Duration Oversight (EDO) of Water Contaminant Features - Withdrawn

This new general permit would allow facilities to hold waste materials such as coal combustion residuals, in perpetuity, under coverage of this permit, and release qualified pollutants to the subsurface, and if found, subsurface-to-surface waters to waters of the state and waters of the United States. Unlined or insufficiently lined basins are deemed pollutant contaminant sources according to Missouri Revised Statute, 644.016(25), RSMo. This permit may only be provided to facilities having undergone a thorough examination of the localized groundwater at the site. This permit does not preclude sites from continuing other operations under other NPDES or state-only permits. The public comment period for the proposed permit conditions ended May 31, 2022. A public meeting was held May 24, 2022. Below are the public comments the department received regarding the draft MO-G330000. At this time, the department is withdrawing the proposed MO-G330000 permit and considering future actions.

Final Site-Specific Permits

Master General Permits

Permit Effective Date Expiration Date Additional Files Description
MO-G010000 Concentrated Animal Feeding Operation (CAFO) Form F – Application for Construction Permit for Concentrated Animal Feeding Operation (CAFO) MO 780-0725

SIC #0211, 0212, 0213, 0214, 0241, 0251, 0252, 0253, 0254, 0259 or 0272

Process wastes are collected and reused as fertilizer by spreading onto agricultural fields at agricultural rates. There is no-discharge except during storms exceeding the design storm event.

*The department is in the process of renewing this permit. 

For more information, visit Concentrated Animal Feeding Operation (CAFO) Permits.

MO-G050000 Abandoned Mine Land Reclamation > 5 Acres MO-G05000 Permit Requirements for Land Reclamation Projects

Form E – Application for General Permit Under Missouri Clean Water Law MO 780-0795

SIC #9512 - Land, Mineral, Wildlife and Forest Conservation

Land reclamation projects involving land disturbance and projects consisting solely of pond and shaft dewatering under control of the department's Land Reclamation Program.

SIC #1629 - Heavy construction, Not Elsewhere Classified

Surface discharges from these reclamation projects will result from rainfall runoff/ impoundment discharges and shaft pumping. Sediment will be controlled during construction with filter fabric, check dams, sediment ponds, straw bales or other Best Management Practices, which will minimize sediment loss.

These projects may also involve stockpiling biosolids for reclamation use. Best Management Practices will be employed at these sites.

MO-G130000 Fish Farms/ Hatcheries

SIC #0273 and 0921

Flow-through Concentrated Aquatic Animal Production Facilities

MO-G140000 Oil/ Water Separators

This permit authorizes the discharge from oil/ water separators and similar waste water treatment devices whose sole function is the treatment of stormwater or water without detergents or additives used to rinse or wash down pavements. This permit applies to establishments such as vehicle repair shops, transformer stations and pipeline compressor stations.

This permit does not apply to establishments that are required to apply for a permit under the stormwater regulations, found in 10 CSR 20-6.200. The permit does not apply to the discharges of wastewater treatment devices for the treatment of vehicle or equipment wash waters.

MO-G220000 Small Meat Processors Form P - Application for MOG22 Processing Meat and Meat Products General Permit Under Missouri Clean Water Law MO 780-2976

SIC #2011-2015 and 2077 

Wastewater, stormwater, surface land irrigation and subsurface soil dispersal from the following industries including, but not limited to, meat first processing (slaughterhouses), meat further processing, renderers, poultry first processors, poultry further processing with SIC Codes #0751, 2011, 2013, 2015 and 2077. These permit conditions incorporate provisions in 40 CFR 432.

MO-G251000 Heat Pumps

SIC #3585, 5084, 1711 and 4961

Discharge from non-recirculating heat pumps, to surface water only.

MO-G350000 Petroleum Storage <250,000 Gallons

SIC #5171

Stormwater discharges from facilities with above ground storage capacity of pre-consumer or post-consumer petroleum products, ethanol or biodiesel totaling more than 20,000 gallons, but less than 250,000 gallons.


MO-G490000 Limestone Quarries

SIC #1411, 1422,1429, 1446 and SIC Major Group Codes 29 and 32

Stormwater and other specified discharges from limestone and other rock quarries, concrete, glass and asphalt industries.

MO-G500000 Sand and Gravel Washing

SIC #1442 and 1446

Discharge of wash water and stormwater from sand and/ or gravel operations.

MO-G640000 Water Treatment Plant Settling Basins

SIC #4941

Water treatment plant filter backwash water and solids and allows operation of no-discharge sludge holding systems. Land application of water treatment plant sludge.

MO-G641000 Zeolite Softeners MO-G641000 Permit Requirements for Zeolite Water Softener Filter Backwash

Form E – Application for General Permit Under Missouri Clean Water Law MO 780-0795

SIC #4941

Discharges of backwash water from water softening units. Zeolite filter backwash discharges.

*The department is in the process of renewing this permit. If this permit is issued to your facility, you must apply for renewal of your permit a minimum of 30 days before its expiration. 

MO-G670000 Hydrostatic Testing of Pipelines and Storage Tanks

All Outfalls- All SIC Codes

Hydrostatic testing of Pipelines and Storage Tanks.

MO-G69000 Dredging Lakes/ River Harbors
Dredging: Return water and stormwater runoff from dredged material deposition sites and other disturbance resulting from maintenance dredging of lakes and rivers.
MO-G698000 Dredging on the Missouri and Mississippi River

 SIC  #144

Discharge of wash water, stormwater and return water from aggregate dredging operations on the Missouri and Mississippi Rivers.

MO-G750000 Car Wash

SIC #7542

Vehicle wash wastewater treatment systems for design flows of 50,000 gallons per day or less. This includes no-discharge land application systems. Provides for 500 gallons per day de minimis exemption under certain conditions.

MO-G760000 Swimming Pools Discharges

SIC  #5999, 7000, 7010, 7030, 7032, 7996, 7997, 7999

Discharge of filter backwash and pool drainage from swimming pools and lined ponds which use chlorine as a sanitizer.

MO-G821000 Land Application of Domestic Wastewater Biosolids

SIC #4952

Land application of domestic septage onto agricultural land for beneficial use as fertilizer and soil amendment for total volume up to 1,000,000 gallons per year that are land applied according to an approved Land Application Management Plan that conforms to the Best Management Practices and other requirements contained in the general permit. Lime stabilization is required prior to land application and application rates shall not exceed 10,000 gallons per acre per year.

*The department is in the process of renewing this permit.

MO-G822000 Land Application of Food Processing Wastewater Form E – Application for General Permit Under Missouri Clean Water Law MO 780-0795

SIC #SIC Codes 200x, 2021-2099 and 5812 - No-Discharge Facility

Land Application or subsurface dispersal system of wastes from the following industries including, but not limited to, SIC 20xx - Light Commercial Food Products Industry and SIC 5812 - Eating Places (restaurant grease traps) onto grass land, crop land or timber land for use as fertilizer and soil amendment.

*Please note, the General Permit applicable to your facility may have changed. SIC Codes 2011-2015 for Meat Products and SIC Code 2077 for Animal and Marine Fats and Oils will receive coverage under the new MO-G220000.

MO-G823000 Land Application of Domestic Wastewater

SIC #4952,6515, 8641

No-discharge, private, domestic wastewater treatment facilities with design flows of less than 50,000 gallons per day.


MO-G840000 Clay Pits

SIC #1455 and 1459

Discharge of stormwater, snowmelt and infiltration water from a clay pit or mine.

MO-G870000 Pesticide Applications

SIC #0851, 4959 and 8999 (including, but not limited to)

Point source discharges of pesticides to waters of the state for the specific pesticide use patterns as defined in this permit. The permit requires that applicators implement site specific control practices and other pest management strategies that are designed to minimize discharges of pesticides to waters of the State.

MO-G920000 Feedstock Compost Sites

SIC #2875

Mixed feedstock composting operations under 20 acres. The operation is to be designed and operated as a no-discharge facility.

*The department is in the process of renewing this permit. 

MO-G940000 Petroleum Impacted Water Remediation

Wastewater and/or stormwater discharges associated with petroleum impacted water at any industrial or commercial facility. 


MO-G970000 Yard Waste Compost Sites

SIC #2875

Stormwater runoff. Flow is dependent upon precipitation. Yard waste composting operations under 20 acres.

MO-GD00000 Non-Publically Owned Treatment Works (POTW) Discharging ≤ 50,000 Gallons Per Day
Non-publically owned treatment works discharging less than or equal to 50,000 gallons per day.
MO-GS10000 State No-Discharge Concentrated Animal Feeding Operation (CAFO)

SIC #0211, 0212, 0213, 0214, 0241, 0251, 0252, 0253, 0254, 0259 or 0272

Process wastes are collected and managed as fertilizer by spreading onto agricultural fields at agricultural rates according to this permit.

*The department is in the process of renewing this permit. 

For more information, visit Concentrated Animal Feeding Operation (CAFO) Permits.

MO-GSE0000 Sewer Extension Construction (GSE)


This permit authorizes the construction of gravity sewer extensions, force mains, and lift stations. Non-earthen flow equalization storage basins at lift stations and inline storage, which flows back into the lift station or collection system, are also included.

Standard Conditions

Standard Conditions for Permits

These minimum conditions apply to all permits where incorporated by reference unless superseded by requirements specific in the permit.

Standard Condition Part I

This document of standard conditions incorporate permit conditions as required by 40 CFR 122.41 or applicable state statues or regulations.  These minimum conditions include sampling, monitoring, and recording; reporting requirements; bypass and upset requirements; and administrative requirements.

Standard Condition Part II

This document of standard conditions notes conditions for publicly owned treatment works specific to industrial users, including definitions, identification of industrial discharges, application information and notice to the department.

Standard Condition Part III

This document of standard conditions outline specific requirements for biosolids and sludge from domestic treatment facilities. This part includes general requirements, definitions, mechanical wastewater treatment facilities, biosolids or sludge disposed at other treatment facility or by contract hauler, incineration of sludge, surface disposal sites and biosolids and sludge lagoons, land application of biosolids, septage, closure requirements, monitoring frequency and record-keeping and reporting requirements.


Pursuant to Section 644.145, RSMo, when issuing permits under this chapter that incorporate a new requirement for discharges from publicly owned combined or separate sanitary or storm sewer systems or publicly owned treatment works, or when enforcing provisions of this chapter or the Federal Water Pollution Control Act, 33 U.S.C. 1251 et seq., pertaining to any portion of a publicly owned combined or separate sanitary or storm sewer system or [publicly owned] treatment works, the Department of Natural Resources shall make a “finding of affordability” on the costs to be incurred and the impact of any rate changes on ratepayers upon which to base such permits and decisions, to the extent allowable under this chapter and the Federal Water Pollution Control Act.

Tools Used by the Department to Determine Affordability

Cost Analysis for Compliance (CAFCom)

The Cost Analysis for Compliance (CAFCom) was developed by the department to meet the requirements of 644.145 RSMo. The CAFCom estimates the potential cost for publicly-owned treatment works to comply with new requirements in a permit. The results of the CAFCom are used to determine an adequate compliance schedule for the permit that may mitigate the financial burden of new permit requirements. The department must consider eight criteria presented in subsection 644.145 RSMo to evaluate the cost associated with new permit requirements.

The eight criteria are as follows:

  1. A community's financial capability and ability to raise or secure necessary funding.
  2. Affordability of pollution control options for the individuals or households at or below the median household income level of the community.
  3. An evaluation of the overall costs and environmental benefits of the control technologies.
  4. Inclusion of ongoing costs of operating and maintaining the existing wastewater collection and treatment system, including payments on outstanding debts for wastewater collection and treatment systems when calculating projected rates.
  5. An inclusion of ways to reduce economic impacts on distressed populations in the community, including but not limited to low- and fixed-income populations. This requirement includes but is not limited to: (a) Allowing adequate time in implementation schedules to mitigate potential adverse impacts on distressed populations resulting from the costs of the improvements and taking into consideration local community economic considerations; and (b) Allowing for reasonable accommodations for regulated entities when inflexible standards and fines would impose a disproportionate financial hardship in light of the environmental benefits to be gained.
  6. An assessment of other community investments and operating costs relating to environmental improvements and public health protection.
  7. An assessment of factors set forth in the United States Environmental Protection Agency's guidance, including but not limited to the "Combined Sewer Overflow Guidance for Financial Capability Assessment and Schedule Development" that may ease the cost burdens of implementing wet weather control plans, including but not limited to small system considerations, the attainability of water quality standards, and the development of wet weather standards.
  8. An assessment of any other relevant local community economic condition.

For further information on CAFComs, please contact the Water Protection Program, Operating Permits Section at 800-361-4827 or 573-751-6825.


The department uses software titled CapdetWorks to estimate the cost for reconstruction of a treatment plant. CapdetWorks is a preliminary design and costing software program from Hydromantis for wastewater treatment plants that uses national indices, such as the Marshall and Swift Index and Engineering News Records Cost Index for pricing in development of capital, operating, maintenance, material and energy costs for each treatment technology. As the program works from national indices and each community is unique in its budget commitments and treatment design, the estimated costs are expected to be higher than actual costs.

The design parameters for Hydromantis are for larger facilities with flows greater than most Missouri facilities are designed for. CapdetWorks provides a cost estimate based on national averages, not the site-specific conditions of a community. Cost estimates are verified through the tracking of actual costs from submitted facility plans, engineering reports, bid documents and loan closures. This verification process allows the engineering section to track costs to see if the assumptions from CapdetWorks are appropriate for the State of Missouri. The department uses CapdetWorks to estimate costs of upgrading to meet new permit requirements in CAFComs.

For further information on CapdetWorks, please contact the Water Protection Program, Engineering Section at 573-751-6621.

Affordability Prescreening Tool

The Affordability Prescreening Tool is a socioeconomic database primarily designed to assist department staff in conducting affordability findings. The data are compiled from the United States Census Bureau and United States Bureau of Labor Statistics. The indicators include population, median household income, per capita income, median age, unemployment rate, poverty level, food stamps reception and consumer price indices. Data are provided for various administrative units including the United States, the State of Missouri, all 114 counties and all 1,039 communities in Missouri for the years 1990, 2000, 2010 and annually beginning in 2011.

Rural Missouri Sustainability Assessment Tool (MoSAT)

The State of Missouri contracted with Wichita State University to complete the Rural Missouri Sustainability Assessment Tool (MoSAT), which is an assessment tool that forecasts rural Missouri community populations and future sustainability. The tool uses a statistical modeling analysis of factors associated with each rural Missouri community that predicts future sustainability changes in each community. A stepwise regression model that was applied yielded 19 individual sustainability factors with statistically significant coefficients. These 19 sustainability factors are valid predictors of rural population change in Missouri and were incorporated into the assessment tool along with overall population changes from 2000 to 2010.

The sustainability factors are:

  1. Change in the population group aged 18 to 29 years from 2000 to 2010
  2. Change in the population group aged 50 and over from 2000 to 2010
  3. Change in the number of persons employed in construction from 2000 to 2010
  4. Change in the number of public assistance income recipients from 2000 to 2010
  5. Change in the number of bachelor’s or higher degree recipients from 2000 to 2010
  6. Change in the number of persons employed in entertainment, recreation and food service from 2000 to 2010
  7. Change in the number of retirement income recipients from 2000 to 2010
  8. Change in the number of Social Security income recipients from 2000 to 2010
  9. Change in the number of persons employed in professional services, scientific and management from 2000 to 2010
  10. Change in the number of high school graduates from 2000 to 2010
  11. Change in the number of persons employed in manufacturing from 2000 to 2010
  12. Change in the number of persons employed in finance, insurance and real estate from 2000 to 2010
  13. Change in the number of persons employed in wholesale trade from 2000 to 2010
  14. Change in the number of persons employed in information technologies from 2000 to 2010
  15. Change in population density (per square mile) from 2000 to 2010
  16. Natural Amenity Scale Rank (1=Low, 7=High)
  17. Change in the number of rural immigrants from 2000 to 2010
  18. Change in the number of persons migrating into the town or village from 2006 to 2010
  19. Change in the number of persons employed in retail trade from 2000 to 2010

The model establishes a hierarchy of the predictive factors which allows it to place a weighted value on each factor. A total of 745 rural towns and villages in Missouri received a weighted value for each of the predicting factors. The weighted values for each rural community within Missouri were then added together to determine an overall decision score. The overall decision scores were then divided into five categories and each town was assigned to a different categorical group based on the overall decision score.

1-2 Likely to see sustainability challenges through time.
3 Sustainable over time but a small change in the social or economic conditions could easily decrease or increase sustainability challenges.
4-5 Shows progress and growth and is likely sustainable over time.

Financial Questionnaire

The Financial Questionnaire is a required attachment to the permit renewal application for publicly-owned treatment works. Along with the Community Supplemental Survey, it collects information on the sustainability and financial capability of the community. Examples of information requested are the “current monthly residential sewer rates” and “property tax collection rate in the municipality.”

For assistance in completing the Financial Questionnaire, please contact the Water Protection Program, Operating Permits Section at 800-361-4827 or 573-751-6825.

Annual Affordability Reports

Annual Reports on Affordability Findings of Compliance to the Missouri Clean Water Law:

Annual Report of Affordability Findings Map

Pursuant to Section 644.145.9, RSMo, the department shall file an annual report by the beginning of the fiscal year with the governor, the speaker of the house of representatives, the president pro tempore of the senate, and the chairs of the committees in both houses having primary jurisdiction over natural resource issues showing at least the following information on the findings of affordability completed in the previous calendar year:

  1. The total number of findings of affordability issued by the department, those categorized as affordable, those categorized as not meeting the definition of affordable, and those implemented as a federal mandate regardless of affordability.
  2. The average increase in sewer rates both in dollars and percentage for all findings found to be affordable.
  3. The average increase in sewer rates as a percentage of median house income in the communities for those findings determined to be affordable and a separate calculation of average increases in sewer rates for those found not to meet the definition of affordable.
  4. A list of all the permit holders receiving findings, and for each permittee the following data taken from the finding of affordability shall be listed:
    • Current and projected monthly residential sewer rates in dollars
    • Projected monthly residential sewer rates as a percentage of median household income
    • Percentage of households at or below the state poverty rate

Permit Renewals

Permittees must submit a completed application for the renewal of a permit at least 180 days prior to expiration of a site-specific permit. The following forms must be included (may need more than one): Domestic wastewater systems are those listed as publicly owned treatment works (POTW), or discharge primarily kitchen and/or bathroom wastewater. Industrial facilities are those having industrial wastewater, including cooling water, and/or stormwater discharges for qualifying industries as found in 10 CSR 20-6.200. Domestic wastewater at industrial facilities is included under the industrial operating permit but additional forms may be required, see below

Completed forms should be submitted via e-mail to For questions, please contact your previous permit writer, the regional office, email, or call the Operating Permits Section at (573) 522-4502.

Other Information