Permits Issuance Process

Missouri Clean Water Law Section 644.051 RSMo establishes timelines for the Department of Natural Resources to render a decision regarding permit applications. Site-specific permits must be either issued or denied within 180 days of the receipt of an application. The timeline is 60 days for 401 certifications and General Permits that do not require a public notice. The department must return application fees when these deadlines are not met.

General Permits

A general permit is a water pollution control operating permit for categories of facilities with similar characteristics. Each general permit has a standard set of conditions and requirements to protect water quality. These conditions are conservative, because a general permit authorizes discharges to most receiving streams throughout the state. It must be protective whether the discharge flows into a lake, a small stream, etc. But some settings are so sensitive that permit conditions become very restrictive. To avoid making all facilities comply with unnecessary conditions, some settings and receiving streams are excluded from a general permit, and facilities wanting to discharge to those sensitive receiving streams are required to obtain site specific permits. One permit is issued, and qualifying facilities apply for coverage under that permit.

For a general permit to be written for a specific type of operating permit, a request should be submitted to the department to develop one. That request is generally initiated by an organization on behalf of a group of industries. Organizations interested in submitting a petition request for development of a general permit should contact the department Water Protection Program permitting section for the information that is needed. A separate authorization is required for each operating location. The general permit is five years in duration, and all facilities authorized to operate under the general permit must apply for renewal at least 180 days before the expiration date of the general permit.

Site-Specific Permits

A site specific permit (also known as an “individual permit”) is written for a specific facility. The conditions of the permit are based on the specific regulations that apply to that facility, the sensitivity of the receiving stream. For these facilities, either there is not a general permit available, or they have sought a site specific permit, or they are required to obtain a site specific permit due to the sensitivity of their receiving stream. These permits usually have a five-year cycle. Most site specific permits are for the discharge of treated wastewater from domestic and industrial facilities. Some facilities land-apply their wastewater rather than discharge it. As with general permits, site specific permits are written to protect Missouri’s numeric and narrative water quality standards. But while general permits are necessarily conservative since they authorize discharges in most settings, site specific permits are written with a specific receiving stream in mind. This means that the conditions and effluent limits are tailored to protection of water quality standards for one receiving stream, and may be more or less stringent than a general permit for a similar activity. Permit conditions for a discharge to a typical Ozark stream may be more stringent than necessary for a discharge to the Missouri River, but may not be stringent enough for a discharge to a losing stream whose flow enters groundwater.

Regional Offices

The department's regional offices review applications for coverage under general permits only. They may also conduct preapplication meetings, site visits and research in support of site specific permits written in the central office.

Central Office

The department's central office writes all site specific operating permits, as well as the General Permits under which Land Disturbance General Permits (also known as construction stormwater permits) are issued through the department's ePermitting web portal.

Permit Renewals

A notice is sent from the department to the permittee that the application for renewal must be submitted 180 days prior to the expiration date on the current permit. When the application comes in it is assigned to a permit writer for review. There are many facets of permit writing, but the common items the permit writer will review include: completeness of the application, if there is an application fee and whether it was paid, facility performance with effluent limits, inspection reports, any impacts to the receiving stream or other water quality assessments. Permit applications are entered into the MoCWIS database for tracking.

Public Notice

All permits are placed on public notice. A public comment period runs for 30 days. A public meeting may also be held if there is widespread public comment with the potential for new information with technical merit for issues relevant to the Clean Water Commission authority. A general permit is put on public notice before issuance or renewal, but issuance of coverage to individual facilities seeking authorization under that general permit are not normally put on public notice. However there are some exceptions. For instance, the first-time issuance of a general permit for a Concentrated Animal Feeding Operation (CAFO) is put on public notice. General permits for airports, chemical manufacturing plants, fabricated structured metal plants, foundries, limestone and rock quarries, lubricant manufacturing plants, petroleum storage facilities greater than 50,000 gallons and wood treaters are required to be placed on public notice prior to issuance for a specific facility by state regulation. All site-specific permits are also put on public notice. Site-specific permits usually have a five-year cycle and are placed on public notice for 30 days prior to issuance or renewal. Sometimes permits are re-drafted and placed back on public notice to resolve major concerns. The department posts draft, site-specific, permits on the internet in order to increase the availability of this information. Comments on the posted permits may be made as described in the public notice. All comments received during the public notice period are considered before issuance of the permit. A summary of any relevant comments and any resulting changes to the permit is provided in the Fact Sheet prior to issuance.

In the event that the department determines it must deny the application for a permit, notice of the denial shall be posted in accordance with state statutes and regulations. If a decision to issue or deny a permit is appealed, the department requests legal representation through the state Attorney General’s Office and initiates hearing officer selection. The Attorney General’s Office may decide to negotiate terms in the permit. If a settlement is not reached, an adjudicatory hearing is held before the Administrative Hearing Commission. The hearing officer makes a recommendation to the Missouri Clean Water Commission on the merits of the appeal. The Clean Water Commission may then direct the department to change a permitting decision, or support the initial decision and leave it unchanged.


Missouri Clean Water Law Section 644.021
Powers and Duties of the Commission, Section 644.036
Prohibited Actions, Section 644.051
Public Hearings, Section 644.066
Public Hearings- how to conduct one, Section 644.116
Rules and Regulations, Section 644.141 Planning Authority, B. Management Authority, C.
Interstate Agencies, D. Termination of Authority; and the department’s rules, Section 6, Permits.