Aquaculture & the Environment



All human activities – from walking through a field to building a skyscraper – have an impact on the environment.  Aquaculture is no exception.  However, modern U.S. aquaculture is far more advanced that both historic practices and practices in many parts of the world.  U.S. regulators and aquaculture practitioners have learned a great deal – from past mistakes and through aggressive research – about how to harmonize aquaculture with the marine environment.

This series of Frequently Asked Questions (FAQs) addresses commonly asked questions about the relationship between aquaculture and the environment.  We discuss U.S. laws and regulations that exist to protect the marine environment as well as specific questions that often are raised about aquaculture’s potential impact.  If you have a question or concern that is not addressed here, contact us.

 1.   What does aquaculture do to protect the environment?

2.    What laws and regulations exist to protect the environment?

3.    What environmental factors are evaluated before a farm is permitted and established in marine waters?

4.    Are drugs and chemicals used in aquaculture?

5.    What causes disease in fish?

6.    What is done to reduce diseases in farmed fish?

7.    What is done to prevent sea lice and other parasites on finfish farms and to minimize impacts on wild fish populations?

8.    What is nutrient discharge and why is it a challenge for finfish aquaculture?

9.    What is done to minimize the impact of fish escapes from aquaculture on wild populations?

10.    What about the potential genetic interaction between farmed and wild fish?

11.    What do aquaculture net-pen operators do to prevent interaction with marine mammals?

12.    Is farmed salmon injected with dye?


 1.  What does aquaculture do to protect the environment?

In the United States, aquaculture is regulated under stringent federal and state laws and regulations that protect the environment.  Through lessons learned over time and by engaging in aggressive research, aquaculture operators have developed commonly-accepted “best management practices” to minimize impacts.  Aquaculture operators are aware that it is in their financial interest to maintain a healthy environment for the fish and shellfish they are growing. Here is a report by the National Ocean Service analyzing and addressing the environmental concerns and recommendations related to cage culture of marine finfish around the world.

In some cases – like shellfish and seaweed farming – aquaculture contributes to environmental health by sequestering nutrients and cleaning up the water. Shellfish Aquaculture and the Environment , a book covering all aspects of shellfish aquaculture, details the role of shellfish farms in provision of ecosystem goods and services. The Executive Summary can be accessed through Connecticut Sea Grant here. In addition to adhering to environmental (and food safety laws), aquaculture operators work with state and federal regulators to continually monitor potential impacts.

2.  What laws and regulations exist to protect the environment?

Aquaculture operators in the United States must abide by a comprehensive suite of environmental regulations, which differ depending on the type of operation.  For operations in marine waters, federal regulations address environmental issues including diseases, discharge, structures, the protection of threatened and endangered species, seafood safety, use of medication, feed ingredients, marine mammal protection, fish habitat, and consistency with state regulations, among others.  Further state and local regulations address these and other issues.  For a table listing most federal statutory authorities for regulation of marine aquaculture, click here.

3.  What environmental factors are evaluated before a farm is permitted and established in marine waters?

For an aquaculture site to be permitted, the operation must show that it will maintain a healthy environment for wild animals in the environment, the animals on the farm, and the surrounding habitat.  Many environmental factors are evaluated before a farm is permitted and continue to be monitored while the farm is in operation.  Such factors include nutrient discharge, protection against escapes of farmed animals, protocols for maintaining fish health, potential impacts to the benthic environment, and many others.

4.  Are drugs and chemicals used in aquaculture?

Rarely.  Because of the success of vaccines to prevent some diseases in farmed fish, the use of antibiotics and other drugs has been reduced dramatically.  While good management practices and vaccines alone are usually enough to prevent or control disease, a farmer may, in consultation with a licensed veterinarian, use a limited number of aquatic animal drugs including antibiotics, in the case where they have been approved by the U.S. Food and Drug Administration (FDA) to treat specific conditions.  In fact, only three antibiotics have been approved for limited use in aquaculture.  Drug use in fish is subject to strict application requirements.  Before a drug is approved for use, FDA requires that it be demonstrated effective, safe for the environment, and safe for humans who consume the treated product. Go to the FDA 'Fish Drug' Q&A.

5.  What causes disease in fish?

Disease can be caused by a number of factors, alone or in combination, which act to weaken the immune system of the animal. Factors may include pathogenic micro-organisms, parasites, environmental influences, aquaculture conditions, and poor nourishment.

6.  What is done to reduce diseases in farmed fish and shellfish?

Fish and shellfish farmers—as well as state and federal regulatory agencies—take many precautions to prevent infection and transmission of pathogens and parasites (which are the agents that cause disease).  At commercial hatcheries, juveniles are reared under carefully controlled conditions to prevent the introduction of disease-causing agents from outside sources.  Before fish or shellfish are transferred to farm sites or released into the wild, veterinarians and other aquatic health professionals evaluate them to ensure that they are free of pathogens or parasites.  Most states also have regulations requiring fish and shellfish to be screened before they are transferred to another site or released into the wild.

Farmed fish are vaccinated against some of the diseases that have caused problems in the past.  Antibiotics are rarely used and, if required, their use is strictly regulated and always under the supervision of a veterinarian.

Did you know?

At NOAA’s Manchester lab in Washington State, fish do not need antibiotics (the lab grows salmon, sablefish, lingcod, and rockfish, among others) because the fish are vaccinated against known pathogens.  Antibiotics can be used on special occasions to treat injuries received when wild fish are captured to be used as brood stock.

7.  What is done to prevent sea lice and other parasites on finfish farms and to minimize impacts on wild fish populations?

Parasites are a fact of life with all forms of animal production, but their presence does not normally cause disease.  The potential harmful effects of parasites can be minimized significantly by following good practices.  The parasite of greatest concern to salmon farmers is sea lice.  Historically, sea lice occasionally have been a problem for farmed salmon in the State of Maine – where they exist naturally in the wild.  Maine has made great strides in minimizing the incidence of sea lice by reducing stocking density, rotating pens among distant locations, and letting sites lie fallow between harvests.

When further treatment is necessary, fish are treated with hydrogen peroxide (which breaks down into water and oxygen) as the first choice and with another compound (similar to that used to de-worm dogs and cats) as a second choice, only as needed.  In the latter case, the fish are moved from their holding structure to a boat with a tank on it; then the fish are treated and replaced in to the structure.  Strict protocols ensure that there is no residual compound in the fish tissue at the time of harvest.  Recently, researchers at University of Maine may have found a way to reduce the spread of sea lice by cultivating local blue mussels alongside salmon farms.  Research in Norway has found that “cleaner” fish (wrass) effectively eat off the parasites from salmon.

Sea lice are not a problem in Washington State due to the lower salinity of the water.  However, there is a gill parasite in Washington that fish farmers treat with a freshwater bath.  Typically, this is done once a year.

8.  What is nutrient discharge and why is it a challenge for finfish aquaculture?

Nutrient discharge from fish farming operations is organic and comes from two sources – fish excrement and uneaten feed that drifts into the water column.  Both types of discharge contain nitrogen and phosphorus – which are biodegradable.  Excretion from farmed fish, like that of wild fish, tends to degrade rapidly and is helped by proper siting of farms.  Arguments are made that waste from fish farms may foul the area under the farm, making it unsuitable for native organisms.  However, this is not the case in the United States, where decades of experience have led to effective management plans, proper siting, and regulatory regimes that ensure minimum impacts to the benthic environment. Some fish farms, such as salmon farms in Maine, fallow between crops to allow the benthos to recover. A review of the effects of cage aquaculture on the marine environment can be found here.

From both regulatory and financial perspectives, strong incentives exist to minimize feed waste.  In some finfish operations, feed represents up to 75% of the operating costs.  Because of the cost of feed and the awareness of the environmental impact of overfeeding, farmers carefully manage feed delivery so as to maximize the growth and well-being of the fish without resulting in wasteful and contaminating excess.

Where does the discharge from fish cages go? In open ocean waters, the wastes are dispersed in the sea and assimilated and recycled by marine bacteria and other organisms.  What was considered a waste is converted into fertilizer and food for algae and seaweed, mollusks, worms, crabs, and other fish.

Did you know?

Salmon farms are managed to preserve species diversity and abundance.   In both Maine and Washington, salmon farms are required to produce “no net enrichment” of bottom sediments.  In Maine, the measure is a change in the benthic community; in Washington, it is determined by chemical analysis.  Both states require recurring benthic video surveys.  Maine manages net pen farms by alternating, or “fallowing” sites; Washington by locating the farms in high current areas over seafloor made of sand, cobble and small rocks.

9.  What is done to minimize the impact of fish escapes on wild populations?

There are two ways that aquaculture fish enter the marine environment – intentionally and unintentionally.  Read more about intentional releases of hatchery fish on our stock enhancement page.

Advanced containment systems and improved management practices – including fish handling in hatcheries and farm management – have dramatically reduced escapes from U.S. fish farms in the last 10 years.  Advances in cage design and technology include stronger net material and improved mooring components.  ‘Best Management Practices’ include the use of underwater cameras to monitor and inspect cages and divers to perform hands-on inspections and maintenance.  If fish do escape, impacts to the genetic diversity of wild fish are minimized by selecting founding hatchery broodstock from local wild fish so the genetic make-up is similar.

Typically domesticated fish that are raised in captivity are poor performers in the wild and few of them are able to reproduce.  However, researchers are now working on methods to make cultured fish sterile so that, if they did escape, they would not be able to breed with their wild cousins.  Further domestication also reduces competitiveness in the wild.

U.S. federal and state permits require containment management systems at all marine sites and enforce these measures through regular inspections and audits.  Equipment and husbandry will continue to evolve and improve as operators test new designs and materials.

10.  What about the potential genetic interaction between farmed animals and wild fish and shellfish?

Genetic interaction between farmed and wild fish and shellfish is another concern related to seafood aquaculture.  Based on years of research and testing, experts are finding that there are many ways to mitigate this risk.  A primary approach is to farm species with genetics similar to -- or very different from -- local wild stocks, depending on the situation.  Aquaculture operators – consistent with federal and state regulatory requirements – reduce the impact of potential cross-breeding through broodstock management, including the use of stocks that are genetically compatible with wild populations.  This is true for hatchery operators for both finfish (for example, salmon and redfish), and shellfish (for example, oysters).

Genetic impacts to wild stocks also are minimized through other strategies:

    Domestication – farmed fish are highly domesticated and do not fare well in the wild.  Hence, the potential for mating and competition with wild stocks is minimized.

    Containment – for netpen aquaculture, advances in cage design are continually decreasing the likelihood of escapes.

    Sterility – for shellfish aquaculture, hatchery practices including manipulation at the larval stage produce bivalves that are reproductively sterile.

Did you know?

The salmon farming industry in Maine follows genetic guidelines for farmed salmon production that mandate the use of local North American stocks that are genetically similar to wild populations, thus reducing the genetic effects from potential interbreeding with wild populations.  Scientists also are looking at the use of sterile hatchery fish to minimize the likelihood that any escapes will reproduce in the wild.

11.  What do aquaculture net-pen operators do to prevent interaction with marine mammals?

The primary deterrent is the use of predator nets. These nets are hung outside of the net-pens and are made of a large, strong mesh that the predator cannot bite through. Bull rails (knee high fences developed by marine mammal biologists to keep sea lions off of docks) are also used to discourage marine mammals from getting onto net pen structures. In extreme cases an electric fence is added to the bull rails.

The Marine Mammal Protection Act (MMPA) prohibits the intentional shooting of marine mammals in commercial fishing operations, which includes aquaculture farms.

12.  Is farmed salmon injected with dye?

No.  In the wild, salmon consume tiny shellfish that contain natural pigments called carotenoids, which are powerful antioxidants and precursors of vitamin A.  These carotenoids, specifically astaxanthin and canthaxanthin, give salmon flesh its distinctive pigment.  Farmed salmon diets are supplemented with natural and/or synthetic astaxanthin similar to the pigment that salmon get in the wild.  Both natural and synthetic astaxanthin are processed and absorbed by wild and farmed fish in exactly the same manner. Carotenoids are good for human health and are used in a wide variety of applications, including as dietary supplements.