Wastewater Permit Writers Manual

Missouri’s Wastewater Permit Writers Manual presents guidance related to water pollution control, including:

• Construction permits
• Operating permits, also known as National Pollutant Discharge Elimination System (NPDES) and/or Missouri State Operating (MSOPs) Permits
  • General permits
  • No-discharge permits
  • Stormwater and land disturbance permits 
• The legal bases, policies and procedures related to them

The permits manual is a tool for department team members writing permits under the Missouri Clean Water Law. It is not intended to answer all questions a permit writer may have, but is a starting point for basic information and a tool to find other resources. It is intended to help all MoDNR offices involved in water pollution control permitting follow the same basic processes and guidelines when drafting permits. Consistency is the goal.

To help our permittees, consultants and other customers better understand the permit process, the department is making the manual available online. We hope permittees and consultants will use the manual to better understand the permit process and aid their communications with our permit writers. We encourage users to help us improve the manual by letting us know of errors and outdated procedures.

Throughout the permits manual, there are information links to federal and state statutes, rules and technical guidance documents that support permit procedures. The numbering and lettering system of the table of contents is not always consecutive. The gaps indicate inactive, reserved topics or appendices. Future manual revisions will result in changes to both the contents and the organizational format and the gaps will disappear.

Chapter 1 – Introduction

• History of the Permitting Program 
• About the Permits Manual

Chapter 2 – Permitting Framework and Scope

2.1 Regulatory Framework

2.2 Scope and Purpose

2.3 Permit Program Areas

• 2.3.1 Municipal and Domestic Sources

  • 2.3.1.1 Secondary Treatment
  • 2.3.1.1.1 Secondary Treatment Equivalent
  • 2.3.1.2 Pretreatment
  • 2.3.1.3 Biosolids
  • 2.3.1.4 Sanitary Sewer Overflows
  • 2.3.1.5 Combined Sewer Overflows
  • 2.3.1.6 Special Discharge Limits

• 2.3.2 Industrial Sources

  • 2.3.2.1 Categorical Industries
  • 2.3.2.2 Primary Industries updated 2014
  • 2.3.2.3 Pretreatment updated 2014
  • 2.3.2.4 Special Discharge Limits

• 2.3.3 Storm Water Sources

  • 2.3.3.1 Land Disturbance
  • 2.3.3.2 Industrial
  • 2.3.3.3 Municipal
  • 2.3.3.4 Special Discharge Limits

• 2.3.4 Animal Feeding Operations (AFO)

  • 2.3.4.1 Unclassified
  • 2.3.4.2 Class II
  • 2.3.4.3 Class IB and IC
  • 2.3.4.4 Class IA CAFOs
  • 2.3.4.5 Special Discharge Limits

• 2.3.5 Construction Permitting

  • 2.3.5.1 Private Domestic Treatment Facilities
  • 2.3.5.2 WPCP-Financed Public Treatment/Transport Facilities
  • 2.3.5.3 Other Public Domestic Treatment/Transport Facilities
  • 2.3.5.4 Sewer Extension Letters of Authorization updated 2014
  • 2.3.5.5 Industrial Treatment Facilities updated 2014
  • 2.3.5.6 (Reserved)
  • 2.3.5.7 CAFOs

• 2.3.6 Exemptions and Waivers

  • 2.3.6.1 Construction Permit
  • 2.3.6.2 Operating Permit
  • 2.3.6.3 Permits-by-Rule Exemptions (Reserved)
  • 2.3.6.4 No-Discharge Permit
  • 2.3.6.5 Small Domestic No-Discharge Facilities
  • 2.3.6.6 CERCLA
  • 2.3.6.7 Permit Waivers

• 2.3.7 Permit Fees

  • 2.3.7.2 SAM II Codes
    • 2.3.7.2.1 Fee Waivers for Modifications
    • 2.3.7.2.2 Modification Fees

• 2.3.8 Domestic Biosolids Management

Chapter 3 – Overview of the Permit

3.1 Types of Permits

• 3.1.1 Site-Specific Permits

• 3.1.2 General Permits

• 3.1.3 Standardized Permits

• 3.1.4 No-Discharge Permits

• 3.1.5 (Reserved)

• 3.1.6 Construction Permits

• 3.1.7 (Reserved)

• 3.1.8 (Reserved)

3.2 Site-Specific Permits

• 3.2.1 Owner, Continuing Authority and Facility

• 3.2.2 Legal Description

• 3.2.3 Receiving Stream and Basin

• 3.2.4 Facility Description

  • 3.2.4.1 (Reserved)
  • 3.2.4.2 Outfall Descriptions
  • 3.2.4.3 Average and Design Flows
  • 3.2.4.4 SIC Codes

• 3.2.5 Effective Date and Expiration Date

• 3.2.6 Signature Authority

• 3.2.7 Effluent Limits

  • 3.2.7.1 Interim Effluent Limits
  • 3.2.7.2 Final Effluent Limits
  • 3.2.7.3 Maximums and Averages
  • 3.2.7.4 Samples and Methods

• 3.2.8 Monitoring and Reporting Frequency

• 3.2.9 Standard Conditions

• 3.2.10 Special Conditions

3.3 General Permits

• 3.3.1 Statewide GP Template

  • 3.3.1.1 Facility Description
  • 3.3.1.2 Applicability
  • 3.3.1.3 Exemptions
  • 3.3.1.4 Requirements and Guidelines
  • 3.3.1.5 (Reserved)
  • 3.3.1.6 Sampling Requirements and Effluent Limitations
  • 3.3.1.7 Records
  • 3.3.1.8 Transfer of Ownership
  • 3.3.1.9 Termination
  • 3.3.1.10 Duty to Comply
  • 3.3.1.11 (Reserved)

• 3.3.2 Facility-Specific Information

  • 3.3.2.1 Name and Address of Permittee
  • 3.3.2.2 Facility Description
  • 3.3.2.3 Effective Date and Expiration Date
  • 3.3.2.4 Signature Authority

3.4 (Reserved)

3.5 No-Discharge Permits

• 3.5.1 Owner, Continuing Authority and Facility

• 3.5.2 Legal Description

• 3.5.3 Receiving Stream and Basin

• 3.5.4 Facility Description

• 3.5.4.1 (Reserved)

  • 3.5.4.2 Outfall Description
  • 3.5.4.3 Average and Design Flows
  • 3.5.4.4 SIC Codes

• 3.5.5 Effective Date and Expiration Date

• 3.5.6 Signature Authority

• 3.5.7 Effluent Limits

  • 3.5.7.1 Interim Effluent Limits
  • 3.5.7.2 Final Effluent Limits
  • 3.5.7.3 Maximums and Averages
  • 3.5.7.4 Samples and Methods

• 3.5.8 Monitoring and Reporting Frequency

• 3.5.9 Standard Conditions

• 3.5.10 Special Conditions

3.6 Permits-by-Rule (Reserved)

3.7 Construction Permits

• 3.7.1 Name and Address of Permittee

• 3.7.2 Facility Description

• 3.7.3 Permit Conditions

• 3.7.4 Effective Date and Expiration Date

• 3.7.5 Signature Authority

3.8 Sewer Extensions

• 3.8.1 Owner, Continuing Authority and Facility

• 3.8.2 Facility Description

• 3.8.3 Letter of Acceptance

• 3.8.4 Letter of Authorization

• 3.8.5 Signature Authority

3.9 (Reserved)

Chapter 4 – Application and Review Process

4.1 Permit Process

• 4.1.1 Site-Specific Permitting

  • 4.1.1.1 Overview
  • 4.1.1.2 Pre-application Activities

• 4.1.2 General Permitting Deadlines

  • 4.1.2.1 Overview
  • 4.1.2.2 Pre-application Activities

• 4.1.3 (Reserved)

• 4.1.4 (Reserved)

• 4.1.5 Transfers

  • 4.1.5.1 Overview
  • 4.1.5.2 Pre-application Activities

• 4.1.6 Variances (See Chapter 9)

• 4.1.7 Modifications

  • 4.1.7.1 Overview
  • 4.1.7.2 Pre-application Activities

• 4.1.8 Terminations

  • 4.1.8.1 Overview
  • 4.1.8.2 Pre-application Activities

• 4.1.9 Revocations

• 4.1.10 Denials

• 4.1.11 Appeals

4.2 Roles of DNR and EPA

4.3 Common Omissions and Errors

4.4 Confidential Information

4.5 WPC Permit Application Deadlines

• 4.5.1 Site-Specific Permit Application Deadlines

• 4.5.2 General Permit Application Deadlines

• 4.5.3 Construction Permit Application Deadlines

4.6 Completing Permit Application Forms

• 4.6.1 Selecting the Correct Application Forms

• 4.6.2 Completing the Required Forms

• 4.6.3 Continuing Authorities

• 4.6.4 Attaching Supplemental Information

  • 4.6.4.1 Additional Construction Permit Requirements
    • 4.6.4.1.1 Plans and Specifications
    • 4.6.4.1.2 Design Guides
    • 4.6.4.1.3 CAFO Neighbor Notice
  • 4.6.4.2 Additional Site-Specific Permit Requirements
    • 4.6.4.2.1 Domestic Biosolids Management Plan
    • 4.6.4.2.2 No-Discharge Management Plan
    • 4.6.4.2.3 POTW Pretreatment Program Submittal
  • 4.6.4.3 Additional General Permit Requirements
    • 4.6.4.3.1 Permit Applicability
    • 4.6.4.3.2 Land Disturbance Storm Water BMP Plan
    • 4.6.4.3.3 Industrial Storm Water SPCCP
    • 4.6.4.3.4 AFO/CAFO Nutrient Management Plan

• 4.6.5 Permit Fees

  • 4.6.5.1 Construction Permit Fees
  • 4.6.5.2 POTW Service Fees
  • 4.6.5.3 Site-Specific Permit Fees
    • 4.6.5.3.1 Private Domestic Fees
    • 4.6.5.3.2 Industrial Permit Fees
  • 4.6.5.4 General Permit Fees
  • 4.6.5.5 (Reserved)
  • 4.6.5.6 Modification Fees
  • 4.6.5.7 Variance Fees

4.7 Review of the Permit Application

• 4.7.1 Logging Receipt of Application and Fees

• 4.7.2 Completeness Check

• 4.7.3 Enforcement Review

  • 4.7.3.1 File Review for Compliance
  • 4.7.3.2 Active Enforcement Case
  • 4.7.3.3 Abatement Orders
  • 4.7.3.4 Settlement Agreements

• 4.7.4 Technical Review

  • 4.7.4.1 Permit Application for New Facility
    • 4.7.4.1.1 General Permits
      • 4.7.4.1.1.1 Land Disturbance
      • 4.7.4.1.1.2 Agricultural Chemical
      • 4.7.4.1.1.3 All Others
    • 4.7.4.1.2 Industrial Permits
      • 4.7.4.1.2.1 (Reserved)
      • 4.7.4.1.2.2 (Reserved)
      • 4.7.4.1.2.3 (Reserved)
      • 4.7.4.1.2.4 Site-Specific Storm Water
      • 4.7.4.1.2.5 CAFO
    • 4.7.4.1.3 Municipal Wastewater Permits
    • 4.7.4.1.4 Domestic Wastewater Permits
    • 4.7.4.1.5 Other Permits
      • 4.7.4.1.5.1 (Reserved)
      • 4.7.4.1.5.2 Permits-by-Rule (reserved)
      • 4.7.4.1.5.3 Permit Variances (reserved)
      • 4.7.4.1.5.4 Subdivision Approvals
      • 4.7.4.1.5.5 De minimis Discharge Approvals
      • 4.7.4.1.5.6 No-Discharge Permits
      • 4.7.4.1.5.7 Municipal MS4 Permits
  • 4.7.4.2 Application for Permit Modification at Existing Facility
    • 4.7.4.2.1 General Permits
      • 4.7.4.2.1.1 Land Disturbance
      • 4.7.4.2.1.2 Agricultural Chemical
      • 4.7.4.2.1.3 All Others
    • 4.7.4.2.2 Industrial Permits
      • 4.7.4.2.2.1 Categorical Industries (reserved)
      • 4.7.4.2.2.2 Primary Industries (reserved)
      • 4.7.4.2.2.3 Non-Categorical Industries (reserved)
      • 4.7.4.2.2.4 Site-Specific Storm Water (reserved)
      • 4.7.4.2.2.5 CAFO
    • 4.7.4.2.3 Municipal Wastewater Permits
    • 4.7.4.2.4 Domestic Wastewater Permits
    • 4.7.4.2.5 Other Permits
      • 4.7.4.2.5.1 LOAs (reserved)
      • 4.7.4.2.5.2 Permits-by-Rule (reserved)
      • 4.7.4.2.5.3 Permit Variances
      • 4.7.4.2.5.4 Subdivision Approvals
      • 4.7.4.2.5.5 De minimis Discharge Approvals
      • 4.7.4.2.5.6 No-Discharge Permits
      • 4.7.4.2.5.7 Municipal MS4 Permits
  • 4.7.4.3 Application for Renewal of Expired Permit
    • 4.7.4.3.1 General Permits
      • 4.7.4.3.1.1 Land Disturbance
      • 4.7.4.3.1.2 Agricultural Chemical
      • 4.7.4.3.1.3 All Others
    • 4.7.4.3.2 Industrial Permits
      • 4.7.4.3.2.1 Categorical Industries (reserved)
      • 4.7.4.3.2.2 Primary Industries (reserved)
      • 4.7.4.3.2.3 Non-Categorical Industries (reserved)
      • 4.7.4.3.2.4 Site-Specific Storm Water (reserved)
      • 4.7.4.3.2.5 CAFO
    • 4.7.4.3.3 Municipal Wastewater Permits
    • 4.7.4.3.4 Domestic Wastewater Permits
    • 4.7.4.3.5 Other Permits
      • 4.7.4.3.5.1 Permits-by-Rule (reserved)
      • 4.7.4.3.5.2 Permit Variances (reserved)
      • 4.7.4.3.5.3 De minimis Discharge Approvals
      • 4.7.4.3.5.4 No-Discharge Permits
      • 4.7.4.3.5.5 Municipal MS4 Permits

4.8 Data Entry

4.9 Draft Review

• 4.9.1 Draft Permit Review Prior to Public Notice

Chapter 5 – Effluent Limits

5.1 Overview

5.2 Effluent Limits/Acute WET Tests, Toxicity Identification Evaluations, and Toxicity Reduction Evaluations

• 5.2.1 Effluent Limits/Acute WET Tests

• 5.2.2 Effluent Limits/WET Tests/Chronic WET tests

5.3 Technology-Based Effluent Limits

• 5.3.1 Non-Domestic Dischargers

  • 5.3.1.1 Legal Foundation
  • 5.3.1.2 Use of Effluent Limitation Guidelines
  • 5.3.1.3 Limitations for Categorical Industries
  • 5.3.1.4 Limitations for Primary Industries

• 5.3.2 Domestic Dischargers

  • 5.3.2.1 Secondary Treatment
  • 5.3.2.2 Equivalent-to-Secondary Treatment
  • 5.3.3 Best Professional Judgement (BPJ) Permit Limits

• 5.3.4 Anti-Backsliding

5.4 Water Quality-Based Effluent Limits

• 5.4.1 Water Quality Review Sheets

  • 5.4.1.1 Determining Need for a WQ Review
  • 5.4.1.2 Requesting a WQ Review

• 5.4.2 Water Quality Reviews

  • 5.4.2.1 Conservative Pollutants
  • 5.4.2.2 Non-Conservative Pollutants
  • 5.4.2.3 Antidegradation

• 5.4.3 TMDL and 303(d) Considerations

  • 5.4.3.1 Contaminants of Concern
  • 5.4.3.2 Permit Limits before TMDL Completion
  • 5.4.3.3 Permit Limits after TMDL Completion

• 5.4.4 Special Water Quality Studies

5.5 Limitations for Specific Waters Based on the Effluent Regulation

• 5.5.1 Missouri and Mississippi Rivers

• 5.5.2 Losing Streams

• 5.5.3 Class L1 Lakes (Drinking Water Lakes)

• 5.5.4 Class L3 Lakes (Other Lakes)

• 5.5.5 Table Rock Lake

• 5.5.6 Lake Taneycomo

• 5.5.7 Metropolitan No-Discharge Streams

• 5.5.8 Outstanding National Resource Waters

• 5.5.9 Outstanding State Resource Waters

• 5.5.10 Subsurface Waters

5.6 Resolution of Conflicting WQ Based Limits

5.7 Effluent Limit/Significant Figures & Rounding: Limit Determination & Discharge Monitoring Reports

Chapter 6 – Monitoring and Reporting Requirements

6.1 Monitoring Conditions

• 6.1.1 Monitoring Locations

• 6.1.2 Monitoring Frequency

• 6.1.3 Sample Collection Methods

• 6.1.4 Analytical Methods

• 6.1.5 Other Considerations

  • 6.1.5.1 Analytical Detection Levels-Definitions
  • 6.1.5.2 Analytical Detection Levels-Compliance Levels
  • 6.1.5.3 Analytical Detection Levels-Total Residual Chlorine
  • 6.1.5.4 Analytical Detection Levels – Cyanide Amenable to Chlorination

• 6.1.6 Requirements for Specific Waters

  • 6.1.6.1 Missouri and Mississippi Rivers
  • 6.1.6.2 Losing Streams
  • 6.1.6.3 Class L1 Lakes (Drinking Water Lakes)
  • 6.1.6.4 Class L3 Lakes (Other Lakes)
  • 6.1.6.5 Table Rock Lake
  • 6.1.6.6 Lake Taneycomo
  • 6.1.6.7 Metropolitan No-Discharge
  • 6.1.6.8 Outstanding National Resource Waters
  • 6.1.6.9 Outstanding State Resource Waters
  • 6.1.6.10 Subsurface Waters

6.2 Reporting and Record Keeping

Chapter 7 – Special Conditions

7.1 Commonly Used Special Conditions

• 7.1.1 Seven Basic Special Conditions

• 7.1.2 Special Studies and Additional Monitoring

• 7.1.3 Best Management Practices (BMPs)

• 7.1.4 Pollution Prevention

• 7.1.5 Compliance Schedules

7.2 Storm Water Discharges Associated with Industrial Activities

7.3 Domestic Facilities

• 7.3.1 All Domestic Dischargers

  • 7.3.1.1 Domestic Biosolids

  • 7.3.1.2 Sanitary Sewer Overflows

• 7.3.2 POTWs Only

  • 7.3.2.1 Pretreatment Program

  • 7.3.2.2 Combined Sewer Overflows (CSOs)

  • 7.3.2.3 Municipal Separate Storm Sewer Systems (MS4)

7.4 AFOs and CAFOs

• 7.4.1 Class IA Site-Specific Permits
• 7.4.2 (reserved)
• 7.4.3 Class IB and IC General Permits

7.5 Land Application and No-Discharge Facilities

Chapter 8 – Standard Conditions of NPDES Permits

Standard Conditions of NPDES Permits

Chapter 9 – Variances

9.1 The Variance Process

9.2 Applications for a Variance

9.3 The Variance Review and Approval Process

9.4 Data Entry

Chapter 10 – Finalizing the Permit

10.1 Documentation for the Draft Permit

• 10.1.1 Documenting the File

• 10.1.2 Fact Sheets

10.2 Public Participation Process

• 10.2.1 Public Notice

  • 10.2.1.1 Permits Requiring Public Notice
  • 10.2.1.2 Permit Modifications
  • 10.2.1.3 Variances
  • 10.2.1.4 Public Notice Process

• 10.2.2 Response to Public Comments

• 10.2.3 Public Hearings and Public Meetings

10.3 Final Permit Actions

• 10.3.1 Permit Issuance

• 10.3.2 Permit Denial

10.4 Data Entry

Chapter 11 - Compendium Documents

11.1 Lagoon Operating Permit Renewal Guidance

11.2 WET Test Revision Memo

11.3 Ammonia Implementation Guidance

11.4 Sanitary Sewer Overflow Implementation

11.5 EPA Memo on Schedules of Compliance

11.6 Low Flow Surveys and Lagoon Operating Permit Renewal Guidance

11.7 MSOP and Fact Sheet Template and Landfill Activities

11.8 Memo of Understanding with Solid Waste Management Program

11.9 Memo of Understanding with Land Reclamation Program

11.10 Incomplete Construction Permit Application Protocol

11.11 Lagoon Concern Investigation - Decision Tree 

11.12 Acceptance of Discharge Monitoring Reports Memo

Appendices

Appendix A - Glossary of Terms

• A.1 General Glossary

• A.2 Construction Site Storm Water Glossary

Appendix B - List of Acronyms

• B.1 General Acronyms

• B.2 Acronyms of Facilities and Owners

Appendix C - Permit Processing Flow Charts

• C.1 Lagoon Permit Renewal Flow Chart

Appendix D - Permit Processing Time Lines

• D.1 General Time-line for all Permits

• D.2 General OP Not Requiring Public Notice

• D.3 CP & OP for New Facilities or Major modifications

Appendix E - Office Responsibility for Permitting

• E.1 Statewide General Permits

• E.2 Issuance of General Permits to Facilities

• E.3 CAFO Permits and LOAs

• E.4 Municipal Permits

• E.5 Domestic Permits

• E.6 No-Discharge Permits

• E.7 Industrial Site-Specific Permits

• E.8 Water Quality Reviews

Appendix F - DNR Signature Authority

• F.1 Operating Permits

• F.2 Construction Permits

• F.3 Letters of Authorization

• F.4 Letters of Approval

• F.5 Denials, Revocations and Waivers

Appendix G - MOUs with Other Agencies and Programs

• G.1 Public Service Commission

• G.2 Department of Health and Senior Services

• G.3 Land Reclamation Program

• G.4 Solid Waste Management Program

Appendix H - Policies

• H.1 Sewer Extension Policy

• H.2

Appendix I - Index to WPC Permitting Regulations and Laws

• I.1 Missouri Clean Water Law

• I.2 Hog Law

• I.3 Regulations

Appendix J - Technical Bulletins and Fact Sheets

• J.1 Biosolids Management

• J.2 Industry-Specific Requirements

Appendix K - List of SIC Codes

• K.1 Categorical Industries

• K.2 Primary Industries

• K.3 Industrial Storm water Requirements

Appendix L - Nine Minimum CSO Controls

Appendix M - CAFO Indemnity Fund and Payments

Appendix N - Permit Conditions

• N.1 Standard Permit Conditions

• N.2 Special Permit Conditions Library

• N.3 Special CAFO Permit Conditions

Appendix O – Reserved

Appendix P - Permit Templates

• P.1 Standardized Templates

• P.2 General Permit Templates

Appendix Q - Samples of Final Permits

Appendix R - Blank Permit Forms

• R.1 Permit Request Forms

• R.2 Permittee Reporting Forms

• R.3 Internal Forms

Appendix S - Samples of Completed Permit Forms

• S.1 Permit Request Forms

• S.2 Permittee Reporting Forms

• S.3 Internal Forms

Appendix T - Total Residual Chlorine Study

Appendix U - Missouri State Operating Permits - Monitoring Frequencies and Sampling Types