​​Section 1: Introduction 

This guide summarizes the requirements for Animal Feeding Operations (AFOs) for the statewide General Discharge Permit administered by the Maryland Department of the Environment (MDE).

About the Permit

The federal Clean Water Act set a goal that America’s waterways be “fishable and swimmable,” and established requirements to manage pollution that could impair federal waters. Maryland enforces those federal requirements within the state under its delegated authority from the US EPA, issuing a new permit every five years as required by federal law and regulations.

Regulated Activities

The permit prevents discharge to waterways by providing conditions for agricultural operations that manage animal waste (manure, poultry litter, and process wastewater). It sets strict rules on when—if ever—a farm can release runoff from its animal areas.

Here’s a simple breakdown of classifications of facilities:

CAFOs (Concentrated Animal Feeding Operations)

• A CAFO’s production area (where thousands of animals are housed or confined) cannot discharge pollutants to surface water—unless there’s an extremely rare storm larger than the 25-year, 24-hour storm event.
• This is a federal standard that applies to most existing CAFOs.

New CAFOs

• New CAFOs are not allowed to discharge pollutants under any circumstances.

MAFOs (Maryland Animal Feeding Operations)

• MAFOs are a Maryland-specific category for operations that typically don’t discharge.
• These operations must meet a zero-discharge requirement—no release to surface waters, no matter how big the storm.

Land Application Areas

• You cannot discharge animal waste or runoff from fields where manure is applied.
• The only exception is stormwater that runs off areas where manure has been spread according to an approved Nutrient Management Plan (NMP).

In short, most existing CAFOs are only allowed to discharge after an extreme storm—one larger than the 25-year, 24-hour storm event. New CAFOs and all MAFOs, however, must meet a strict zero-discharge requirement. In practice, this means your operation should be designed and managed to prevent runoff under nearly all weather conditions.

Why You Need A Permit

1. It’s the Law: Federal law (the Clean Water Act) prohibits discharging pollutants to U.S. waters without an authorizing permit. MDE is authorized to administer this program in Maryland.
2. Enforcement Authority: The U.S. EPA maintains concurrent enforcement authority for clean water violations.
3. Required Plan Enforceability: Once MDE grants coverage, the terms and conditions outlined in your required plan become legally enforceable terms and conditions of the permit.
4. Efficiency: This general discharge permit structure reduces the paperwork burden by streamlining the process for less impactful activities.
   
   

Section 2: Step-by-Step Guide to Compliance 

Step 1: Apply for Coverage

To obtain authorization, eligible applicants must submit the following:

1. Notice of Intent (NOI) Form: A signed copy of the form.
2. Required Plans: Submit the plans (see Step 2).
3. Applicable Fees: Submit the necessary fees, which now specifically include application fees and annual fees for all CAFOs.
4. Existing Permittees: If you are currently registered, you must submit a completed NOI and applicable fees. We will determine if your existing required plan is current. If modification is needed, we will notify you, and the updated plan is due within 90 days of the request.
5. Electronic Submittal: Applications will be required to be submitted electronically after December 21, 2025 unless a waiver is granted.

Step 2: Develop and Implement the Required Plan

Your operation must develop, submit, and implement a site-specific required plan.

• What is the Required Plan? It is a Comprehensive Nutrient Management Plan (CNMP), or a Nutrient Management Plan (NMP) and a Soil Conservation and Water Quality Plan (“CP”). Note that the conservation plan has been added to the definition of "required plans.”
• Plan Goal: The plan must identify and describe the practices you will implement to assure compliance with the effluent limitations and special conditions of the permit.
• Standards: The plan must meet federal standards (40 CFR 122.42(e)) and must be consistent with all requirements of the Maryland Department of Agriculture (MDA) regulations. You must use Maryland NRCS Practice Standards.

Key Requirements for Your Required Plan (Nine minimum standards):

Your plan must include procedures to address the following critical areas:

• Signature and Retention: The plan must be signed by the applicant (owner/operator) and the plan writer. A current copy must be kept on-site.

Step 3: Ongoing Compliance, Monitoring, and Reporting

• Inspections: For poultry operations, inspections still need to occur even between flocks, including waterline inspections. Click here​ for required self inspection and recordkeepinging templates.
  
• Annual Reporting: You must submit an Annual Implementation Report by March 1 of every year.
• Notification of Noncompliance: Noncompliance notifications can now be submitted via email.
  
  

​Section 3: Important Updates

The draft permit includes clarifications and some substantive changes from the expiring permit. Below is an overview:

A. Clarifications to Definitions and Required Actions

• Animal Confinement Time:  Clarifies that if an animal is confined for any portion of the day, it is considered to be on the facility for a full day. The 45 days in a 12-month period do not need to be consecutive, nor do they need to be the same animals.
• Practice Standards: All references to NRCS Practice Standards have been changed to Maryland NRCS Practice Standards to ensure clarity that the standards are specific to Maryland and exclude any that are not approved by the state.
• Required Plans: The definition of "required plans" now explicitly includes the Soil Conservation Plan and Water Quality Plan.
• Mortality Management: Clarifies requirements for CAFOs using incinerators or composters for mortality management.
• Silage Leachate: The requirements now specifically mention silage leachate as a pollutant.
• Feathers/Particulates: Feathers and other particulates now have a separate section.

B. Required Actions

• Potholes and Stormwater: There is a new requirement for pothole management and preventing the commingling of stormwater with manure, litter, and process wastewater.
• Winter Application: MDE must be notified prior to any land application of process wastewater while winter restrictions are in place.

C. Changes to Operational Size and Status

• House Square Footage: A change in house square footage can change an operation size from medium to large.
• Non-Organic to Organic: Changing from a non-organic operation to an organic operation is a modification.
• Number of Animals: A change in the number of animals that does not result in a medium-to-large shift is still considered a modification. A change from a large to medium operation is also considered a modification.

D. Transferring Manure and Operation Ownership

• Transferring Manure/Waste: When CAFO or MAFO-generated manure, litter, or process wastewater is sold or given away, the permittee must comply with specific requirements that document the transfer and promote proper management. For example, the federal requirement to provide a recipient with a nutrient analysis is specifically listed as a permit requirement.
• Transfer of Ownership: The permittee must notify MDE at least 30 days prior to a transfer of ownership. The new owner/operator must submit the required plans to us within 90 days of the transfer date. A person who fails to follow the transfer process cannot operate as a CAFO or MAFO.

E. Substantial Changes to the Required Plan (Requiring Public Notice)

If you make changes to your required plan, we will review them to determine their impact. If the changes are considered significant or substantial, they must go through the public participation process. Substantial changes include, but are not limited to:

1. New Land Application Areas: Adding new land application areas not previously included in the plan (with limited exceptions).
2. Changing Application Rates: Changing the field-specific maximum annual rates (pounds of nitrogen and phosphorus).
3. Adding New Crops/Uses: Adding any crop or other uses not included in the plan.
4. Increased Risk of Transport: Changes to site-specific components of the plan that are likely to increase the risk of nitrogen and phosphorus transport to waters of the U.S.

F. Opportunity for Public Input

MDE has scheduled a public comment period concerning the tentative permit determination from October 3, 2025, to January 3, 2026.

Written comments must be submitted by January 3, 2026, to MDE, Attn: Alexis Capes, or via email at [email protected]. Ensure you include the permit number.