Alaska Aquaculture Permitting

Lease and permit information for commercial marine aquaculture activities

Permits for commercial marine aquaculture activities

Application Instructions

How to Apply

Step-by-Step Instructions for the Local, State, and Federal Aquaculture Permitting Process

The Alaska Aquaculture Permitting Process (see image to the right), developed by the Alaska Interagency Working Group, is a flowchart of the local, state, and federal permitting processes.

    • There are five steps to the process.

    • Each step has additional components. See the information that flows from each step (left to right) in the chart.

    • Each step labeled in the flow chart tiers to the numbered steps in the written instructions below.

    • To minimize possible delays later in the permitting process, complete Steps 1-2:  Plan Your Project and Local Permitting Process before submitting formal applications with the state or federal agencies.


  • The following information is organized into five steps, with more detailed components in each section:

Aquaculture Permitting Flowchart
Alaska Aquaculture Permitting Process. Click to view larger image.

Review and complete the steps on the Getting Started guidance page and the Siting Your Farm guidance page to: a) avoid user conflicts; b) make sure your proposed site is in an area that follows relevant regulatory city, state, and federal guidelines and requirements; and c) create your site maps and diagrams according to state and federal application requirements.

Contact State and Federal Agencies and set up Pre-Application meeting (see Before You Start)

  •   ADNR – aquatic farm lease information
  •   ADF&G – aquatic farm operation and other permits
  •   ADEC – shellfish growing area classification, shellfish harvester and other permits, and water quality certification
  •   USACE – nationwide permit, individual permit, or letter of permission
  •   USCG – private aids to navigation (PATON)

step 2 flow chartStep 2. Local Permitting ProcessYou may need an authorization from a municipality or borough if your farmsite is within borough or municipal boundaries. If you plan to use uplands in your operation, prior permission from the adjacent upland owner must be obtained (keep in mind that this process varies greatly from city to city, refer to the Getting Started information, and work closely with your local planning commission).

2a.  Contact the Local Planning Commission.

2b.  Aquaculture Approved Zoning District. Find out if your proposed site is in an Aquaculture Approved Zoning District. If not, amend the proposal.

2c.  Conditional Use Application Review for Completeness. Stand by for Planning Commission review of application completeness – you may need to provide more information.

2d.  Conditional Use Permit Approved.

2e.  Planning Commission Approval.

step 2 flow chartProspective farmers are required to submit a State Joint Agency Aquatic Farm Application along with the application fee. The application fee amount depends on the size of the proposed farm and can be found in the fee schedule (An application opening period is scheduled every year from January 1 through April 30. Note: it is possible for the agencies to decide not to open the application period in a given year, but unlikely). The application is used by ADNR, ADF&G, and ADEC to determine your proposal’s feasibility.

3a.  Submit the State Joint Agency Application to ADNR with required application fee.

3b.  Application Reviewed for Completeness. Stand by for ADNR and ADF&G review of application completeness – you may need to provide more information or modify the application.

3c.   Shellfish on Bottom Culture: ADF&G Site Survey Scheduled and Fee. If you are planning on bottom culture to grow clams, ADF&G will contact you to schedule an initial site survey (this can add up to a year of review time).

Table 1. Joint Agency Application Fees

Joint Agency Application Fees
Joint Agency Application Fee>1 acre: $600
1-3 acres: $1200
>3 acres: $2000
One-time fee

Wild Stock Survey for Shellfish on-bottom cultureFee calculated per day/per site, location and site-size dependent. Fee may be as high as $5000

3d.  Agency Notice and Review Period. ADNR leads and coordinates the review, giving other agencies 20 days to review your proposed project. Agencies can request more time if needed. You will also receive the ADF&G initial review and recommendation regarding the Operation Permit proposal at this point.

3e.  Results of Biomass Survey (1 year): For on-bottom clam culture, ADF&G will conduct a site biomass survey to determine the existing population of shellfish to be cultured. Depending on the results of the survey, site specific conditions may be included in your permit to meet harvest and restoration of wildstock requirements.

3f.   Preliminary Decision. ADNR makes a preliminary decision (PD) based on your application information and agency input. This will include a recommended decision about your application and your development plan for public review. 

NOTE: Submit your USACE application after receiving a Preliminary Decision on your State Joint Agency Application (see Step 5).

3g.  Public Notice/Agency Review (30 Days). ADNR provides a 30-day public comment and review window of the preliminary decision.

3h.  Final Finding and Decision Issued. ADNR makes a Final Finding and Decision (FFD) based on public notice input and all previously received information. You will receive the ADNR final Administrative Order and Decision, including terms of lease if approved.

3i. Appeal Period (20 Days). If your application is denied, you have a 20-day period to appeal the ADNR Final Finding and Decision. Anyone else who commented during the 30-day public comment period can also appeal the decision, whether it was an approval or denial.

3j. Final Finding and Decision. Decision becomes a Final Administrative Order on the 31st day after issuance.

3k.  Fees, Bonding, and Insurance Provided. Aquatic Farm Lease Issued. Receive, sign, notarize, and return ADNR lease. Make sure to also include: first annual lease fee, proof of liability insurance, and performance guarantee bond. ADNR will then send you a finalized signed lease after you complete. Your lease is conditionally valid for 10 years.

Table 2. ADNR Lease and Associated Fees

ADNR Lease and Associated Fees ADNR Lease and Associated Fees
Annual Lease Fee$450 for the first acre plus an additional $125 per acre or portion thereof 30 acres. See ADNR fee schedule for farms >30 acres.
Performance Guarantee BondMinimum $2500
Proof of Liability InsuranceBased on quote from insurance company or broker.

3l. Aquatic Farm Operation Permit Decision. ADF&G will approve or deny an Aquatic Farm Operations Permit (AFOP) within 30 days of the Aquatic Farm Lease being issued. A person adversely affected by the commissioner’s decision (either approval or denial) has 30 days to ask for reconsideration only if the person has new or additional information relevant to the decision.

3m. Aquatic Farm Operation Permit Issued. The AFOP will include requirements that must be adhered to for the length of the 10-year permit. The permit must be signed and the signature page returned to ADF&G. An annual report is required to be submitted to ADF&G by January 31 of the following year of each year of operation.

Additional ADF&G Permits that may be necessary:

3n.  Special Area Permit: If you’re farming in Kachemak Bay, you’ll need a Special Area Permit (SAP). Go to ADF&G Special Area Permits – Refuges, Sanctuaries, and Critical Habitat for more information and the application. Once an Aquatic Farm Operation Permit is approved, ADF&G can issue the SAP. The application does not require an additional fee.

3o.  Acquisition Permit: An Aquatic Stock Acquisition and Transport Permit is required to acquire wild stock for the purpose of providing broodstock or seedstock to an aquatic farm or hatchery, or to acquire wild stock for culture at an aquatic farm or hatchery. To request approval, use the Aquatic Stock Acquisition and Transport Application and submit it to the department at least 30 days before the proposed acquisition.

3p.  Transport Permit: A Stock Transport Permit is required to import or transfer seed stock to, from, or between an aquatic farm and hatchery in Alaska. ADF&G must issue a Stock Transport Permit before shipment of any seedstock may occur. To request approval to transport seed stock, use the Stock Transport Permit Application form and submit it to the department at least 45 days before the requested date of transport. Pathology samples may be required to be submitted.


step 4 flow chart

If you’re growing shellfish you’ll need a Shellfish Growing Area (SGA) classification as part of receiving your operational permit from ADEC. You will also need Shellfish Harvester Permit and potentially a Shellfish Dealer Permit depending on what you plan to do with your products. For seaweed, you’ll need the Aquatic Plant Food Establishment Permit if you’re doing more than harvesting and trimming your crop. It is important to note that you may start the shellfish growing classification step sooner, in order to expedite the total length of your application process. However, you may risk taking on the costs of a year of testing only to have your project denied in the joint agency application process.

Shellfish Growing Area (SGA) Classification (process can take up to 1 year). Contact ADEC Shellfish Program Manager for an Application for the Initial Sanitary Survey to Classify a Proposed Shellfish Growing Area. Note: payment of the $500 initial classification fee is required with submission of the application (see Table 1). An operator will be expected to collect water samples and pay for shipping to the ADEC laboratory in Anchorage. More information can be found here.

Table 1. ADEC Shellfish Growing Area Classification Fees

ADEC Shellfish Growing Area (SGA) Classification Fees
Initial Classification$500 one-time fee
Annual Reapproval of Classified Areas$150 for each day ADEC conducts SGA re-approval activities

Once your application is submitted, it will go through the following process:

  1.  Site Boundary Determination: Boundaries are determined considering topography, sources of natural and human contamination, and potential for additional growing areas nearby. ADEC obtains this information from the State of Alaska Aquatic Farms Application, information you provide in your Operational Permit application, and using existing data from ADF&G shellfish inventory studies.
  2.  Shoreline Survey and Identification of Potential Contaminants: ADEC will conduct a shoreline survey to identify potential contaminants in the area by considering various physical and biological site characteristics.
  3. Water Quality Sampling MOU: Proposed growing or harvesting area waters must be tested to assure they meet fecal coliform standards in the National Shellfish Sanitation Program (NSSP). Note: Water quality samples may be collected by an operator through a Memorandum of Understanding (MOU) with ADEC.
  4. Sanitary Survey Report: Information from steps 1-3 will be compiled into a sanitary survey report, culminating in a Shellfish Growing Area Classification.
  5. Shellfish Growing Area Classification: The classification area can be approved, conditionally approved, conditionally restricted, prohibited, or restricted. The classification of the SGA (see Table 2) is determined by the water quality data collected and analyzed from samples collected over a minimum of year. Samples are collected throughout a minimum of a year period to provide an idea of water quality of the area throughout the year. All areas must be reclassified every year. In Alaska, the most common SGA Classification is “Approved” or “Conditionally Approved,” but this is dependent on ADEC water sample review.

    Table 2. SGA Classification and Definitions

    SGA ClassificationDefinition
    ApprovedA growing area where harvest for direct marketing is allowed.
    Conditionally ApprovedA growing area which meets the criteria for the approved classification except under certain conditions described in a management plan.
    Conditionally RestrictedA growing area that meets the criteria for the restricted classification except under certain conditions described in a management plan.
    ProhibitedA growing area where the harvest of shellstock for any purpose is not permitted. Unclassified areas are treated as areas classified as Prohibited.
    RestrictedA growing area where harvesting shall be by special license and the shellstock, following harvest, is subjected to a suitable and effective treatment process through relaying or depuration.
  6. Growing Area Status Assignment: The Growing Area Status will be designated as open, closed, reopened, remote, or seasonally remote and may change during a harvest period. See Table 3 for details.

    Table 3. Growing Area Status Assignment Definitions

    OpenShellfish may be harvested subject to its classification.
    ClosedResult of sewage spill, biotoxin levels or emergency.
    ReopenedEmergency abated, fecal coliforms, biotoxin levels or other contaminants returned to acceptable levels
    RemoteLack of human habitation, not impacted by actual or potential pollution source
    Seasonally RemoteArea is classified as approved but a closure period is defined. One sample required before reopening.
  7. Shellfish Harvester/Dealer Permit. An ADEC Operational Permit is required to harvest shellfish or sell their products from a SGA classified as Approved or Conditionally Approved. You can find the applications for harvester and dealer permits here. Dealer permits are only required for farmers who are processing products beyond harvest.

i. Submit Application and associated fee (see table 5 for fees).

ii. Complete and Submit Proof of Harvester or Dealer training.

iii. Other requirements: Depending on which permit you apply for, you may need to submit additional materials such as the Seafood Plan Review Checklist (for shellfish dealers). You can find a list of other potentially required materials here. Information about Hazard Analysis Critical Control Point (HAACP) and Sanitation Standard Operating Procedure (SSOP) requirements can be found here. Contact ADEC Shellfish Program Manager for assistance. Shellfish Harvester/Dealer Permit: An ADEC Operational Permit (see Table 4) is required to harvest shellfish or sell their products from a SGA classified as Approved or Conditionally Approved. Download the application for harvesters here. Download the application for dealers here. Dealer permits are only required for farmers who are processing products beyond harvest.

Table 4. Types of shellfish operations

Type of OperationDefinition
Shellfish HarvesterA person who takes shellstock by any means from a growing area. Harvesters may only sell product to permitted shellfish dealers in Alaska
Shellstock ShipperA dealer who grows, harvests, buys, or repacks and sells shellstock. They are not authorized to shuck shellfish nor to repack shucked shellfish. A shellstock shipper may also buy, repack, and sell in-shell product as well as ship shucked shellfish.
Shellstock ReshipperA person who purchases shellfish from dealers and sells the product without repacking or relabeling to other dealers, wholesalers, or retailers
Shucker-PackerA person who shucks and packs shellfish. A shucker-packer may act as a shellstock shipper or reshipper or may repack shellfish originating from other certified dealers.
Shellfish RepackerAny person, other than the original certified shucker-packer, who repackages shucked shellfish into other containers.
Geoduck Dive VesselA vessel used to hold and transport harvested geoducks for market

Table 5. Operation type and associated permit application and fee

Type of OperationPermit ApplicationAnnual Fee
Geoduck Dive VesselGeoduck Dive Vessel Application$162.00
Shellfish HarvesterShellfish Harvester Application$162.00
Shellstock ShipperShellfish Dealer Application$162.00
Shellstock ReshipperShellfish Dealer Application$162.00
Shucker-PackerShellfish Dealer Application$649.00
Shellfish RepackerShellfish Dealer Application$325.00

8. Aquatic Plant Food Establishment Permit: If you’re growing aquatic plants AND processing them beyond harvest and trimming: you will need to obtain a food establishment permit from ADEC. This permit is required for processes such as freezing, drying, and packaging the product. 

It is recommended that if you are pursuing a Letter of Permission, or Individual Permit, that you submit your USACE application after you have received initial approval (a preliminary decision) from the State, and the project description is finalized (review Step 3). This helps avoid the need to resubmit your application if changes to your proposal occur as a result of feedback from the public or state agencies during the state permitting process. If you are pursuing a Nationwide Permit, you are required to submit a copy of the ADNR preliminary decision with your Preconstruction Notification to the USACE. 

  1. Complete the USACE Application for the USACE Permit for all permit types or the Nationwide Permit Pre-construction Notification for nationwide permits (no associated fee unless receiving an IP, approximate review time 60-120 days).
  2. Follow instructions and submit via email to or in person at your local Regulatory Field Office. Follow the USACE application map instructions in the Siting Your Farm section to make sure you have included all required information. Note that your application will be reviewed using one of three pathways depending on your project: a Nationwide Permit (NWP), an Individual Permit (IP), or a Letter of Permission (LOP).
  3. Once your application has been received, a project manager is assigned to your application process for the duration.

Other Applicable Laws, Permits and Consultations 

Under section 7(a)(2) of the Endangered Species Act (ESA), the USACE must consult with the National Marine Fisheries Service (NMFS) and/or U.S. Fish and Wildlife Service (USFWS) on activities that may affect a listed species or designated critical habitat. In addition, Essential Fish Habitat (EFH) consultation with NMFS, or a National Historic Preservation Act (NHPA) consultation with the State Historic Preservation Office (SHPO) and other consulting parties may be required. While the applicant does not conduct these consultations, they may be required to provide information to the USACE, and can help front load their applications by considering adding best management practices to further reduce their projects potential impacts to listed species and habitat. Learn more about the consultation process for NMFS and EFH and ESA best management practices by visiting Aquaculture Permitting in Alaska | NOAA Fisheries page. 

For projects reviewed as Letters of Permission or Individual Permits, a Clean Water Act Section 401 Water Quality Certification (WQC) from ADEC may be required. When you submit for your USACE authorization, you should also request a “prefiling meeting” with ADEC (or EPA if proposing to farm in waters near Annette Island/Metlakatla). No sooner than 30 days after you request a prefiling meeting with ADEC/EPA you can apply for a WQC. You should include (carbon copy or “cc”) the USACE on all requests made to ADEC/EPA. ADEC/EPA will decide whether a WQC is required, not required, or waived for your project. Information on how to request a prefiling meeting with ADEC and apply for a WQC can be found on the ADEC website.  For projects in waters around Annette Island/Metlakatla, a prefiling request can be emailed to the EPA at EPA will instruct applicants how to apply for a WQC.

Your project may require a Private Aid to Navigation (PATON) permit from the USCG depending on the location and components of your farm. Contact District 17 PATON Manager at (907) 463-2272 or Todd Buck, USCG Marine Information Specialist, at (907) 463-2269 or to receive help in determining if your project will require a PATON. 

Nationwide Permit (processing time up to 60 days): NWPs are permits issued nationwide, typically every five years. When applying for a NWP, the USACE verifies that the proposed project fits the terms and conditions of the NWP. The USACE has issued three NWPs which authorize specific types of mariculture projects:

  • NWP 48 – Commercial Shellfish Mariculture Activities;
  • NWP 55 – Seaweed Mariculture Activities; and
  • NWP 56 – Finfish Mariculture Activities (not legal in Alaska state waters)

Additional information on these NWPs can be found on USACE’s website.

NWPs provide the most efficient permitting option if your project qualifies.

  1. If your application is deemed incomplete, you will be asked to provide more information. 
  2. Any required consultations must be completed.
  3. USACE will complete a memo for record.
  4. USACE will issue a decision.

Individual Permit (processing time up to 120 days): An IP is most often used for projects that are large in scale and may involve more substantial environmental impact. If an IP is required, a permit fee of up to $100 is collected at the time of permit issuance.

  1. If your application is deemed incomplete, you will be asked to provide more information. 
  2. Public Notice and Comment Period. The project manager will draft and share a public notice, evaluate the impacts—both to the public and the environment—of the project, consider all comments received, negotiate modifications to the project if necessary, and draft appropriate documentation to support a recommended permit decision. A Public Interest Review will be based on public comment and analysis of other relevant factors. The project manager will determine if the project conflicts with public interest. If the project is deemed not in the public interest, it will not be approved.

General criteria considered are:

  • Relevant extent of public and private needs
  • Practicality of using alternative locations and methods to accomplish project purposes (in cases where unresolved conflicts of resource use exist)
  • Extent and permanence of beneficial and detrimental effects the proposed project may have on the public and private uses for which the area is suited
  • Coordination of Project. Any required consultations (see the Other Applicable Laws, Permits, and Consultations section above) must be completed
  • USACE will complete a memo for record
  • USACE will issue a decision

If your application is denied, you have 60 days to submit an appeal request for the decision. During the appeal review, a site visit and/or appeal conference may be coordinated. Once a final decision is made, it cannot be re-appealed. More information about the appeal process can be found 33 CFR part 331.

Letter of Permission (LOP) – decision to issue will take up to 120 days: An LOP is currently the most commonly used form of approval for aquaculture projects from USACE and is deemed sufficient for relatively small-scale projects where the proposed work would be minor, would not have significant individual or cumulative impacts on environmental values, and should encounter no appreciable opposition.

  1. If your application is deemed incomplete, you will be asked to provide more information. 
  2. Agency & Adjacent Property Owner Comment Period (15 Days) and Coordination of the Project (see the Other Applicable Laws, Permits, and Consultations section above).
  3. USACE will complete a memo for record
  4. USACE will issue a decision

If your application is denied, you have 60 days to submit an appeal request for the decision. During the appeal review, a site visit and/or appeal conference may be coordinated. Once a final decision is made, it cannot be re-appealed. More information about the appeal process can be found here