Aquaculture Permitting Guide

(I wrote this for a nonprofit group interested in promoting aquaculture.  They wanted a guide to the permitting process that you have to go through to become a shellfish farmer. I tried to write a condensed, easy to read guide -in contrast to the outdated and hard to read government produced guide. I simplified it so that a fishermen or other layperson could understand what they needed to do to go through the complicated permitting process.)


The Joint Programmatic General Permit

This is the permit that you need to submit to get your aquaculture operation going—the only time you don’t need it is when you’re using the traditional bottom culture method without any gear or structures in the water.

This is a combined permit that is sent to all thIMAG0067e agencies that need to look at it before you get the OK to start your aquaculture operation. They include the State’s Bureau of Aquaculture, the Office of Long Island Sound Programs, The DEEP’s Marine Fisheries Division, the DEEP’s Boating Division, The Army Corp of Engineers, and, if necessary, the local municipal shellfish commissions. Seems like a lot but most of these agencies are only looking at a few specific parts of your application.

The key to the permitting process is to write your application so that the permitting agencies will be comfortable with approving it. You want to be able to accomplish your goals, but need to reduce the risk that the State assumes when they approve your project. Remember, the land you lease is public land, and the state government has to ensure that it is used responsibly.

The easiest way to successfully permit your operation with the least headache possible is to work with the agencies through the process. No permitting guide can give you all the information you need—it is up to you to contact and work with the State to be successful.

The Business Plan

You’ll want to have at least a rough idea of what you want to do when you start this process. There are a few guides available on Connecticut Sea Grant’s website that can help you with this. You’ll need to know what you want to grow, what habitat it likes to grow in, what techniques and gear you need, and how big your operation is going to be. Don’t forget to account for growth of your business. You don’t want to start too small and leave no room for growth or diversification. You should have as clear a plan as possible to help the permitting agencies understand what you want to do.

Site selection is a critical part of this process. If you choose a poor site, you may be relegated to slow growth, inconvenient site location, and rough working conditions. Take into consideration tides, currents, and prevailing winds when you are comparing sites. Make sure you do your homework and choose more than one suitable area for your operation. This way, you won’t be scrambling to find another site if your first choice doesn’t work out.

Ok, let’s take a look at some of the agencies you’ll be talking to when you go through the permitting process.

The State Department of Agriculture’s Bureau of Aquaculture-
The lead agency—the one you’ll be dealing with the most—is the State Department of Agriculture’s Bureau of Aquaculture. These are the people you’ll send your permit to. They’re in charge of leasing state lands to the growers. They also monitor water quality, classify shellfish water, find sources of pollution, and license shellfish operations, research, and education. You’ll submit your permit to them and they will distribute it to other agencies for review. The Bureau of Aquaculture is your primary point of contact in this process.

The things they don’t do are: regulating water intake and discharge systems from aquaculture systems (like hatcheries), and regulating floating and underwater structures.

The other agencies and offices:

CT DEEP’s Office of Long Island Sound Programs (OLISP)
This part of the DEEP is responsible for making sure that your operation complies with Connecticut’s Coastal Management Plan.
Taken from their website, “the Program ensures balanced growth along the coast, restores coastal habitat, improves public access, protects water-dependent uses, public trust waters and submerged lands, promotes harbor management, and facilitates research. The Coastal Management Program also regulates work in tidal, coastal and navigable waters and tidal wetlands…” Think of this office as a sort of steward of the Sound.

CT DEEP’s Navigation Safety/Boating Division-
If a boat can pass through your area and you plan on leaving gear in the water- then this division will want to see your permit. You’ll have to fill out a Marker Permit Application.

CT DEEP’s Marine Fisheries Division
This division will review your application and consider your planned operations’ effects on the native fish and habitat in the Sound. They’ll also examine its impact on commercial and recreational fishing.

CT DEEP’s Waste Management and Compliance Assurance Permitting Division
If you plan on having a water intake and/or discharge (like a hatchery), then you may need a permit from this division.

US Army Corp of Engineers (USACE)
This federal Agency is concerned with the same things as the DEEP Boating division—parts of your permit that may cause a hazard or impede navigation.

Local Municipal Shellfish Commissions
These groups will only be involved if your activities take place within town waters. They’ll review the application and submit their comments to the Bureau of Aquaculture.

Getting Through the Process

It may seem like a daunting task getting your permit through all of these agencies. It’s not, as long as you approach the process the right way. Some may think of this in the way you’d apply for a job—just gather all the paperwork, do your research, mail it in and hope for the best. This permitting process won’t work well if you approach it this way. The chances are pretty slim that your permit will be approved if the only time any regulators see it is when it comes to them as a “finished” application. Be prepared to have a lot of extra work, expense, and frustration redesigning your plans if you don’t first talk to the people who have the authority to approve your permits.

Each of these agencies has points of contact. Before you start, talk to them—starting with the Bureau of Aquaculture. Explain your ideas: what you plan to do, where you want to be, when you want to start. They’ll help you along the way. Then, when you submit the finished permit applications, it won’t be foreign to the people who make the yes-or-no decisions on it. It will be complete and take into account all the recommendations they made to you during the process.

Other people that can help: Connecticut Sea Grant-
A group that’s worth getting to know is the Connecticut Sea Grant. They are a federally funded part of the National Oceanic and Atmospheric Administration (NOAA) that helps to promote and educate people about the aquaculture industry. They have many different publications and offer consulting and training services to people interested in aquaculture.

Getting a lease

If you’re leasing an area, this must be finished before the application can be approved. The Bureau of Aquaculture is the agency that issues leases. You’ll want to develop a rough idea of what you want to do, pick a few suitable sites, then schedule a meeting with the Bureau of Aquaculture. You can discuss your plans with them and they will research your potential sites to see if there are conflicts with other lease holders. You can also get their help to fill out the lease application form to start the process. You can see an example of a lease on their website.
To start your site selection research, you can use the Shellfisheries Mapping Atlas that is provided by the Connecticut Sea Grant. You can find it on their website ( With this tool you can identify grounds that are suitable for growing shellfish and are not currently being leased by another grower. It allows you to overlay leases, municipal beds, and shellfish harvesting areas onto a chart.

HACCP Certification-

Hazard Analysis and Critical Control Points, or HACCP, is training required by the FDA. People who produce and/or sell food need to have this training. If you are growing shellfish, kelp, or anything else for sale as a food product, then you need to take the training course. It will teach you how to properly handle your products to ensure consumer safety, and how to develop an HACCP plan—which is used to document safe food handling practices. The class is offered by CT Sea Grant—you can view the future class dates, times, and locations on their website.

The Actual Application

You should try to answer as many of these questions as you can before you meet with the Bureau of Aquaculture. This way you’ll have as much information and material as you can get initially, and can minimize your meetings with the Bureau.