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 We encourage users to help us improve the manual by letting us know of errors and outdated procedures.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

Chapter 2 – Permitting Framework and Scope

2.1 Regulatory Framework

2.2 Scope and Purpose

2.3 Permit Program Areas

Chapter 3 – Overview of the Permit

3.1 Types of Permits

3.2 Site-Specific Permits

3.3 General Permits

3.4 (Reserved)

3.5 No-Discharge Permits

3.6 Permits-by-Rule (Reserved)

3.7 Construction Permits

3.8 Sewer Extensions

3.9 (Reserved)

Chapter 4 – Application and Review Process

4.1 Permit Process

4.2 Roles of DNR and EPA

4.3 Common Omissions and Errors

4.4 Confidential Information

4.5 WPC Permit Application Deadlines

4.6 Completing Permit Application Forms

4.7 Review of the Permit Application

4.8 Data Entry

4.9 Draft Review

Chapter 5 – Effluent Limits

5.1 Overview

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

5.3 Technology-Based Effluent Limits

5.4 Water Quality-Based Effluent Limits

5.5 Limitations for Specific Waters Based on the Effluent Regulation

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

6.2 Reporting and Record Keeping

Chapter 7 – Special Conditions

7.1 Commonly Used Special Conditions

7.2 Storm Water Discharges Associated with Industrial Activities

7.3 Domestic Facilities

7.4 AFOs and CAFOs

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

10.2 Public Participation Process

10.3 Final Permit Actions

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


Appendix A - Glossary of Terms

Appendix B - List of Acronyms

Appendix C - Permit Processing Flow Charts

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

Appendix J - Technical Bulletins and Fact Sheets

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

Appendix Q - Samples of Final Permits

Appendix R - Blank Permit 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