Connecticut's Aquaculture Permitting Process

shellfish graphic
General Overview

Aquaculture is the rearing, cultivation and harvest of aquatic plants and animals in controlled marine-based culture systems. According to the National Oceanic and Atmospheric Administration, aquaculture is the fastest growing form of food production in the world, and U.S. production is estimated at $1 billion annually and growing. This sharp increase in product demand by consumers translates into demand to establish and develop new aquaculture sites by growers. This trend holds true in Connecticut, as the aquaculture industry has expanded both traditional and experimental technologies to raise scallops, oysters, clams, and mussels. In order to ensure appropriate development and use of our waterways, a number of state and federal agencies, including the Connecticut Department of Energy and Environmental Protection (DEEP), are charged with regulating aquaculture development. This guide provides an overview of the regulatory authorities and outlines the permitting requirements for those interested in pursuing aquaculture in Connecticut.

Within the DEEP there are several divisions responsible for planning, reviewing and regulating different aspects of aquaculture development, including in-water gear and structures, water discharges, navigational safety, and recreational and commercial fisheries.

Agency Coordination

In order for an application for aquaculture structures to be successful, an applicant should consult with the various local, state and federal regulatory agencies that share a role in shaping acceptable aquaculture activities. These agencies include the local shellfish commissions, the DEEP, the US Army Corps of Engineers (ACOE) and the Connecticut Department of Agriculture, Bureau of Aquaculture (DA/BA). To ensure a seamless, multi-agency regulatory review of proposed aquaculture activities, a single permit application form was developed by the DEEP, DA/BA and ACOE.

DEEP Land & Water Resources Division mussels

Within the DEEP, the Land & Water Resources Division (LWRD) is responsible for regulating structures in tidal, coastal and navigable waters and within tidal wetlands under the Structures, Dredging and Fill Act and the Tidal Wetlands Act. This regulatory agency reviews aquaculture activities with an eye towards protecting critical habitats and species and balancing the various recreational and commercial uses and aesthetic values of Long Island Sound.

LWRD is also responsible for reviewing aquaculture applications to determine whether a project may be exempt from permit review. Upon receipt of a complete application, LWRD staff determine whether the activities proposed by the applicant are exempt or non-exempt. Generally speaking, an exempt aquaculture project is one that is located on a leased or designated shellfish bed and does not interfere with navigation in the area. An example of an exempt aquaculture activity would be a set of shellfish bottom cages in an area where no navigational impacts are anticipated. A non-exempt project is one that is located outside of a leased or designated shellfish bed and does interfere with navigation.

Following review of an aquaculture application by LWRD and determination of whether the proposed activity is exempt or non-exempt, the applicant will receive a letter indicating whether a permit is required and additional steps that must be taken. At the same time, the ACOE will conduct a coordinated review with other state and federal agencies, as appropriate. After the initial review process, applicants will be notified in writing within 45 days of any additional requirements or required information. Once the appropriate authorizations are received from the DEEP and ACOE, the DA/BA will issue a Certificate for Aquaculture Operations to the applicant.

Please note that written authorization from the Connecticut Department of Energy and Environmental Protection, the Army Corps of Engineers, and the Connecticut Department of Agriculture, Bureau of Aquaculture must be received before aquaculture activities can commence or gear can be placed in the water.

DEEP Boating Division, Navigation Safety/Boating
grow out tray

The DEEP Boating Division, Navigation Safety/Boating Access Unit is responsible for planning, developing and implementing the Navigation Safety program, which includes the marking of aquaculture structures when necessary. The Boating Division reviews all aquaculture proposals for navigation safety and boating access. Specifically, this Unit determines whether a proposed project can potentially be a hindrance or danger to navigation. If so, the applicant will be instructed to mark the area with information or danger buoys, as appropriate.

Additionally, the applicant will be informed whether they are required to submit a regulatory marker permit application to Boating Division. The applicant should be aware that if a boat is able to transit the area where aquaculture structures are proposed to be placed, they will likely be required to obtain a marker permit. It is recommended that prior to the submittal of an aquaculture application to DA/BA, the applicant contact Division staff for information about the permit and the permitting process associated with it.

Once the Boating Division receives a complete marker permit application, the applicant will be contacted to schedule a field inspection of the area to be marked. During this site meeting, modifications to or discussions with regard to the buoy arrangement may occur. After the inspection, and provided there are no further concerns, the Division will issue approval to install the required buoys and gear.

DEEP Marine Fisheries Division

The DEEP Marine Fisheries Division is responsible for regulating recreational and commercial fisheries for finfish, squid and arthropods (lobster and crabs) in Connecticut’s marine waters, with the goal of maintaining sustainable fisheries and fish populations. To this end, the Division regulates various aspects of those fisheries, including types and placement of fishing gear, minimum and maximum sizes, possession limits, seasons, landings at Connecticut’s ports, and certain aspects of handling product in the marketplace.

The Marine Fisheries Division also reviews applications for aquaculture proposals for potential effects on fish and fish habitat, as well as effects on the commercial and recreational fisheries under the Division’s jurisdiction. Comments on applications, including recommendations to avoid or minimize adverse effects on resources and fisheries, are sent by the Marine Fisheries Division to LWRD for consideration in making a permit decision.

DEEP Bureau of Materials Management and Compliance Assurance
flow-through tank

The Bureau of Materials Management and Compliance Assurance’s Water Permitting and Enforcement Division has been delegated by EPA under the Clean Water Act to administer the Discharge Permitting Program in Connecticut. All discharges, including those from aquaculture facilities such as hatcheries, whether directed to surface waters, groundwaters, or to sanitary sewers, are subject to permitting under this program.

Discharges to surface waters are administered under the National Pollutant Discharge Elimination System (NPDES), whether the discharge is directed to a dedicated outfall pipe, through a municipal stormwater drainage system, or through any other conveyance. Discharges under this program are subject to specific chemical monitoring and must also be non-toxic. For example, flow-through rearing waters at hatcheries would be expected to be covered by a NPDES permit with minimal treatment requirements. More heavily impacted wastewaters such as tank cleaning waters would require more advanced treatment and would probably not be suitable for direct discharge.

Discharges to a sanitary sewer system (or in some cases, discharges hauled to an approved sewage treatment plant) are administered under the state’s Pre-treatment Program. Where sanitary sewers are available, heavily impacted waters such as tank cleaning wastewater or specialty wastewaters from activities such as disinfection or intensive disease treatment should be directed to the sewer.

Discharges to groundwater are administered under the Underground Injection Control Program. This program covers large septic systems with design flows greater than 5,000 gallons per day (gpd), agricultural waste disposal, landfill leachate and certain soil and groundwater remediation discharges. This option should generally be reserved for sites where sanitary sewers are unavailable and site conditions are amenable for wastewater assimilation. Where sewers are available, certain discharges such as leachate from composting may still be appropriate for ground discharge.

Please note that any individual who discharges water, substances, or materials into the waters of the State is required to obtain a permit prior to commencing the discharge. Waters of the State include all surface and groundwaters, and sanitary and storm sewers. Subsurface discharges of domestic sewage which are not community sewer systems and which have a volume of less than 5,000 gallons per day (gpd) are regulated by the State or local health departments in accordance with the State Health Code. Volumes greater than 5,000 gpd are regulated by DEEP.

It should also be noted that DEEP intends to issue a General Permit that will cover discharges to surface waters, groundwaters and sanitary sewers for aquaculture activities. Terms, conditions and limits in this general permit are expected to be similar to those required in individual permits for these activities.

Local Agencies
installation plan

Connecticut's municipal Shellfish Commissions are responsible for managing shellfish resources, shellfisheries and aquaculture in town waters which lie north of the State Jurisdiction Line. Each commission is required to develop a comprehensive management plan that includes a process for leasing commercial shellfish grounds and providing local review of applications for placement of aquaculture structures in town waters.

Although these local decision-makers do not have legal authority to permit aquaculture structures, the Commissions play a role in the review process for potential social and use conflicts, as well as potential effects on protected habitats and/or species caused by aquaculture activity. If projects are located in municipal waters, the local Shellfish Commission is consulted. Comments received from the local Shellfish Commission with regard to aquaculture applications are typically sent to DEEP OLISP during the application review process.

Aquaculture Resources

All application forms and other technical and regulatory information can be found at University of Connecticut Sea Grant Commercial Aquaculture webpage. For more detailed information relating to the regulatory interaction with the aquaculture industry in Connecticut, please refer to A Guide to Marine Aquaculture Permitting in Connecticut (PDF) developed by Connecticut Sea Grant, DEEP, DA/BA and ACOE.

Contact Information for Permitting Agencies

696 Virginia Road
Concord, MA 01742

P.O. Box 97
Milford, CT 06460

79 Elm Street
Hartford, CT 06106

CT DEEP/Marine Fisheries Division
P.O. Box 280
Old Lyme, CT 06371

CT DEEP/Navigation Safety/Boating Access Unit
P.O. Box 280
Old Lyme, CT 06371

CT DEEP/Water Permitting and Enforcement Division
79 Elm Street
Hartford, CT 06106

Connecticut Sea Grant College Program
University of Connecticut
1080 Shennecossett Road
Groton, CT 06340-6048

This overview is designed to answer general questions and provide basic information. You should refer to the appropriate statutes and regulations for the specific language of the different regulatory programs. This document should not be relied upon to determine whether an environmental permit is required. It is your responsibility to obtain and comply with all required permits.

This brochure was funded by the National Oceanic and Atmospheric Administration.

Illustrations by: Tom Ouellette

Click on Connecticut's Aquaculture Permitting Process to view this brochure as a PDF document.

Content last updated on February 27, 2020