Frequently Asked Questions and Answers
7/22/2025
1. Why hasn’t MDEQ finalized the January 2025 proposed State Water Alteration Program regulations?
The Mississippi Department of Environmental Quality (MDEQ) proposed rules in January 2025 to start building the State Water Alteration Program (SWAP), which is designed to regulate impacts to Mississippi streams, wetlands, and other surface waters classified as waters of the State (WOTS). These draft rules—considered Phase I of the program—outlined tools like exemptions and conditional exemptions but did not yet include the full program framework. The full program would include delineation and permitting rules in Phase II and training and program implementation in Phase III.
During the public comment period, including a hearing held on April 17, 2025, many stakeholders expressed concern that they could not give full feedback without seeing the entire program, including how permitting and mitigation would work. MDEQ agrees that more detail is needed and has decided not to finalize the initial proposal. Instead, MDEQ is working on a more complete set of rules covering things like how waters will be identified (delineation), how permits will be issued, and what mitigation may be required. There will be additional opportunities for public input before and after MDEQ proposes this more complete set of rules.
2. What is MDEQ’s authority for developing a waters of the State regulatory program? Why is it important to have this kind of program in Mississippi?
Mississippi law (Mississippi Code § 49-17-29) requires anyone who might pollute waters of the State (WOTS) or place materials in a way that could lead to pollution of WOTS to get a permit or an exemption from the Mississippi Department of Environmental Quality (MDEQ). For many years, most projects altering Mississippi’s streams, wetlands, and other waters through dredging or filling needed a permit from the U.S. Army Corps of Engineers issued under the Clean Water Act (Section 404) because the majority of state waters were also federally protected as waters of the United States. MDEQ would review these projects and issue a Water Quality Certification to ensure the permitted activities met Mississippi’s water quality standards. Water Quality Certifications helped protect these waters while also meeting state permitting requirements.
However, a 2023 U.S. Supreme Court decision (Sackett v. EPA) changed which waters are federally protected. Many waters in Mississippi that were once covered by federal permitting are no longer included; these are now considered “waters of the State only” (WOTS-only). This shift left a regulatory gap: certain waters in Mississippi that used to be protected by both federal and state oversight now rely solely on state law for protection.
By developing and implementing the SWAP program, MDEQ aims to foster wise development while preserving the vital roles WOTS play in supporting clean water, wildlife, fish, and aquatic life, as well as domestic, agricultural, industrial and recreational activities. Without this program, many of Mississippi’s wetlands, streams, and other sensitive waters could be permanently altered or degraded with no oversight. That could lead to an increase in impaired waters, reduced water quality, drainage issues, and a decline in the ability of natural systems to handle pollution (assimilative capacity). These impacts don’t just harm the environment—they can also lead to higher costs for communities, obstacles to future economic development, and losses in fishing, seafood production, recreation, and outdoor activities.
3. I understand why we need to “fill the gap” and protect waters of the State that are not also waters of the United States, but isn’t MDEQ already doing something about that? What’s wrong with the current approach?
The Mississippi Department of Environmental Quality (MDEQ) currently requires Antidegradation Reports for activities that could impact waters of the State that are not also federally protected waters of the United States. While this helps ensure some level of review, it’s not a complete or consistent solution.
The current approach relies on case-by-case analysis and doesn’t provide a clear or predictable path for applicants or MDEQ. It can add time and uncertainty to the permitting process and doesn’t offer a long-term framework for managing and protecting waters of the State. With the State Water Alteration Program, MDEQ plans to develop a tiered permitting system with different levels of oversight to build clarity, efficiency, and flexibility into the permitting process.
4. Is MDEQ expanding the definition of waters of the State?
No. The Mississippi Department of Environmental Quality (MDEQ) is not expanding the definition of waters of the State. In the January 2025 proposed regulations, MDEQ clarified components of the definition in three ways. MDEQ clarified that:
- Permanent, intermittent, and ephemeral waters are included in the definition of WOTS.
- “Wholly landlocked” surface waters in the definition of WOTS means those waters that are “entirely surrounded by land and never have an inlet from other surface waters or an outlet to other surface waters.”
- The term “privately owned” in the definition of WOTS means “owned by a single individual, partnership, or corporation.”
5. Are any waters excluded from the definition of waters of the State?
Yes. While Mississippi’s definition of waters of the State is broad and covers most surface waters, including any surface water that is classified as a water of the United States, there are specific exceptions in the definition.
A lake, pond, or other surface water is excluded from the definition of waters of the State if it meets all three of the following conditions:
- it is entirely surrounded by land, and it never has an inlet from other surface waters or an outlet to other surface waters;
- it is owned by a single individual, partnership, or corporation; and
- federal regulatory authorities have determined that it is not a water of the United States. (Remember, all waters of the United States are also considered waters of the State.)
In addition to waters meeting these three criteria, there are some artificial water features that MDEQ does not consider WOTS. Examples include swimming pools, sewage treatment lagoons, and certain man-made channels that carry only treated wastewater.
6. How did MDEQ determine the proposed thresholds for impact size to qualify for a conditional exemption under the State Water Alteration Program? Will the Department consider modifying any of the proposed thresholds?
As part of building the State Water Alteration Program (SWAP), the Mississippi Department of Environmental Quality (MDEQ) is designing a tiered permitting system. This system includes different levels of oversight—ranging from conditional exemptions to general permits to individual permits—depending on the type of activity and how much it affects waters of the State (WOTS) as measured in either linear feet (for streams and channels) or acres (for wetlands and similar waters).
In determining thresholds to qualify for a conditional exemption MDEQ is considering the question, “At what point does a project’s impact on waters of the State become large or complex enough that it no longer makes sense to offer the most streamlined and flexible permitting option—both in terms of the application process and approaches to protecting water quality?” This question helps MDEQ find a balance: making it easier for smaller, lower-impact projects to move forward with less paperwork and faster approvals, while reserving more detailed reviews for larger or more complex activities.
MDEQ may revisit the January 2025 proposed conditional exemption thresholds as it further develops and refines the tiered permitting framework for SWAP.
7. Will MDEQ consider activities and eligibility criteria for exemptions or conditional exemptions other than those included in the January 2025 proposed regulations?
Yes. MDEQ is reviewing the activities and eligibility criteria identified for exemptions and conditional exemptions in the January 2025 proposed regulations to determine if other common types of activities should also qualify for a more streamlined review and permitting process. In particular, MDEQ is evaluating whether additional activities could fit under one of three simplified permitting paths:
Exemptions – for activities previously exempt from permitting and routine activities with little or no potential for significant and long-term negative impacts to human welfare and/or the environment
Conditional Exemptions – for frequently occurring activities with minimal or predictable impacts, as long as they meet specific impact size limits and environmental safeguards
General Permits – for frequently occurring activities that have low to moderate impacts and can be authorized using a standard set of conditions
The goal is to ensure that frequently occurring and lower risk activities can continue efficiently while still protecting the quality and health of Mississippi’s waters.
8. What if my project potentially impacts both waters of the United States and waters of the State?
MDEQ’s goal is for its review of projects potentially affecting both waters of the United States and waters of the State to happen through a single, combined process if possible. One tool MDEQ is considering for meeting this goal is a single application that serves as both a SWAP permit application and a Water Quality Certification request. MDEQ is working to ensure that the process for reviewing and permitting projects affecting both federal and state waters is as streamlined and coordinated as possible and avoids unnecessary paperwork or delays.
Important Updates – MDEQ Waters of the State Regulations
5/12/2025
MDEQ completed the public notice and hearing for the proposed State Water Alteration Program (SWAP) regulations on April 17th, 2025. Based on comments received during the public notice period, MDEQ will not finalize the regulations as proposed. MDEQ will further develop regulations to address impacts to Waters of the State, including regulations for delineation, mitigation, and permitting. MDEQ anticipates proposing updated regulations in the late fall of 2025 with an additional opportunity for public comment.
MDEQ continues to encourage engagement in the process. Please send recommendations and suggestions to MDEQ at WOTS@mdeq.ms.gov.
Public Notice for State Water Alteration Program (SWAP) Regulations
1/3/2025
MDEQ is proposing regulations to provide clarity and consistency to the existing definition of waters of the State and to establish the State Water Alteration Program (SWAP), which will include exemptions and conditional exemptions for activities that could affect waters of the State (i.e., agricultural and silviculture activities; ditch maintenance activities; ditch reshaping activities; activities addressed under a Section 401 Water Quality Certification; emergency response operations; Linear Transportation Activities; Utility Line Activities; and Residential, Commercial, and Institutional Development Activities).
Any interested party may submit comments regarding these proposed regulations by submitting the comments in writing to the Mississippi Department of Environmental Quality, Attention: Waters of the State, MDEQ, P.O. Box 2261, Jackson, MS 39225. In order to be considered, written comments should be delivered to the Department of Environmental Quality by the end of business on April 17, 2025.
Notice of Public Hearing
A public hearing regarding the proposed regulations will be conducted on Thursday, April 17, 2025, at 1:00 p.m. in the Commission Hearing Room of the Department of Environmental Quality, 515 East Amite Street, Jackson, Mississippi, 39201. The public is invited to attend and ask questions to gain information regarding the proposed regulations and/or to present verbal or written comments on the proposed regulations.
MDEQ will be livestreaming the public hearing. The ability to ask questions and submit comments during the event will be limited to in-person attendees. To register for the livestream, please visit https://us06web.zoom.us/meeting/register/QLPI3S2vQB2xckkpW3J4bw#/registration.
