Editing Fish farming (section)

== Issues ==
{{See also|Aquaculture of salmon#Issues}}
{{Bar chart|title=Mean [[Eutrophication|eutrophying emissions]] (water pollution)<br>of different foods per 100g of protein<ref name="Nemecek 987–992">{{Cite journal|last1=Nemecek|first1=T.|last2=Poore|first2=J.|date=2018-06-01|title=Reducing food's environmental impacts through producers and consumers|journal=Science|volume=360|issue=6392|pages=987–992|doi=10.1126/science.aaq0216|issn=0036-8075|pmid=29853680|bibcode=2018Sci...360..987P|doi-access=free}}</ref>|float=right|label_type=Food types|data_type=Eutrophying emissions (g PO<sub>4</sub><sup>3-</sup>eq per 100g protein)|bar_width=20|width_units=em|data_max=360|label1=[[Beef]]|data1=365.3|label2=[[Aquaculture|Farmed fish]]|data2=235.1|label3=[[Aquaculture|Farmed crustaceans]]|data3=227.2|label4=[[Cheese]]|data4=98.4|label5=[[Lamb and mutton]]|data5=97.1|label6=[[Pork]]|data6=76.4|label7=[[Poultry]]|data7=48.7|label8=[[Egg as food|Eggs]]|data8=21.8|label9=[[Faboideae|Groundnuts]]|data9=14.1|label10=[[Peas]]|data10=7.5|label11=[[Tofu]]|data11=6.2|label12=|data12=|label13=|data13=}}
{{Bar chart|title=Mean [[greenhouse gas emissions]] for different food types<ref>{{Cite journal|last1=Michael Clark|last2=Tilman|first2=David|date=November 2014|title=Global diets link environmental sustainability and human health|journal=Nature|volume=515|issue=7528|pages=518–522|doi=10.1038/nature13959|pmid=25383533|bibcode=2014Natur.515..518T|s2cid=4453972|issn=1476-4687}}</ref>|float=right|label_type=Food types|data_type=Greenhouse gas emissions (g CO<small>2</small>-C<small>eq</small> per g protein)|bar_width=20|width_units=em|data_max=62|label1=[[Ruminant|Ruminant meat]]|data1=62|label2=[[Recirculating aquaculture system|Recirculating aquaculture]]|data2=30|label3=[[Trawling|Trawling Fishery]]|data3=26|label4=[[Aquaculture|Non-recirculating aquaculture]]|data4=12|label5=[[Pork]]|data5=10|label6=[[Poultry]]|data6=10|label7=[[Dairy]]|data7=9.1|label8=[[Fishery|Non-trawling fishery]]|data8=8.6|label9=[[Egg as food|Eggs]]|data9=6.8|label10=[[List of root vegetables|Starchy roots]]|data10=1.7|label11=[[Wheat]]|data11=1.2|label12=[[Maize]]|data12=1.2|label13=[[Legumes]]|data13=0.25}}

=== Welfare ===
There is a growing consensus that [[Pain in fish|fish can feel pain]].<ref>{{Cite web |last=Johnston |first=Ian |date=2017-04-10 |title=Pescatarians warned they are eating 'sentient animals' who form friendships, after landmark study on fish |url=https://www.independent.co.uk/news/science/fish-sentient-animals-friends-positive-emotions-study-study-source-ethics-eating-pescaterians-vegans-a7660756.html |access-date=2024-07-10 |website=The Independent |language=en}}</ref><ref>{{Cite web |last=Woodruff |first=Michael |date=3 July 2020 |title=Fish are nothing like us, except that they are sentient beings |url=https://aeon.co/essays/fish-are-nothing-like-us-except-that-they-are-sentient-beings |access-date=2024-07-10 |website=Aeon |language=en}}</ref> Despite the vast number of fish consumed, fish welfare has historically received little attention.<ref name=":3">{{Cite web |last=Torrella |first=Kenny |date=2021-03-02 |title=The next frontier for animal welfare: Fish |url=https://www.vox.com/future-perfect/22301931/fish-animal-welfare-plant-based |access-date=2024-07-10 |website=Vox |language=en-US}}</ref>

Farmed fish are usually raised in overcrowded environments, making them susceptible to stress, injuries, aggression and diseases. These conditions prevent them from engaging in natural behaviors such as nesting or migration. Overcrowding often leads to poor water quality due to fish waste and antibiotics use. [[Sea lice]] infestations are common and can cause painful lesion, but are typically treated with harsh chemicals. Additionally, fish are genetically engineered to grow larger and faster, leading to health problems such as [[Cataract|cataracts]] and abnormal heart shapes.<ref name=":3" />

=== Feeding ===
{{Bar chart|title=Mean [[Acid rain|acidifying emissions]] (air pollution)<br>of different foods per 100g of protein<ref name="Nemecek 987–992"/>|float=right|label_type=Food types|data_type=Acidifying emissions (g SO<sub>2</sub>eq per 100g protein)|bar_width=20|width_units=em|data_max=350|label1=[[Beef]]|data1=343.6|label2=[[Cheese]]|data2=165.5|label3=[[Pork]]|data3=142.7|label4=[[Lamb and mutton]]|data4=139.0|label5=[[Aquaculture|Farmed crustaceans]]|data5=133.1|label6=[[Poultry]]|data6=102.4|label7=[[Aquaculture|Farmed fish]]|data7=65.9|label8=[[Egg as food|Eggs]]|data8=53.7|label9=[[Faboideae|Groundnuts]]|data9=22.6|label10=[[Peas]]|data10=8.5|label11=[[Tofu]]|data11=6.7|label12=|data12=|label13=|data13=}}
The issue of feeds in fish farming has been a controversial one. Many cultured fishes (tilapia, carp, catfish, many others) can be raised on a strictly herbivorous diet. Top-level carnivores (most [[salmonidae]] species in particular) on the other hand, depend on fish feed, of which a large portion is usually derived from wild-caught fish ([[anchovies]], [[menhaden]], etc.). Vegetable-derived proteins have successfully replaced fish meal in feeds for carnivorous fishes, but vegetable-derived oils have not successfully been incorporated into the diets of carnivores. Research is underway to try to change this, such that even salmon and other carnivores could be successfully fed with vegetable products. The F3 Challenge (Fish-Free Feed Challenge),<ref name="herox.com_F3">{{Citation |year=2017 |title=F3 Fish-Free Feed Challenge |url=https://herox.com/F3 |access-date=2017-02-07 |postscript=.}}</ref> as explained by a report from ''[[Wired (website)|Wired]]'' in February 2017, "is a race to sell 100,000 metric tons of fish food, without the fish. Earlier this month, start-ups from places like Pakistan, China, and Belgium joined their American competition at the Google headquarters in Mountain View, California, showing off feed made from [[seaweed]] extracts, [[yeast]], and [[algae]] grown in [[bioreactor]]s."<ref name="Molteni_2017-02-05">{{Citation |last=Molteni |first=Megan |date=2017-02-05 |title=Inside the race to invent a fish-free fish food |journal=[[Wired (website)|Wired]] |url=https://www.wired.com/2017/02/taking-fish-fish-food/ |access-date=2017-02-07 |postscript=.}}</ref>

Not only do the feeds for carnivorous fish, like certain salmon species, remain controversial due to the containment of wild caught fish like anchovies, but they are not helping the health of the fish, as is the case in Norway. Between 2003 and 2007, Aldrin et al. examined three infectious diseases in Norwegian salmon fish farms—heart and skeletal muscle inflammation, pancreas disease, and infectious salmon anemia.<ref>{{Cite journal|last1=Aldrin|first1=Magne|last2=Storvik|first2=Bård|last3=Frigessi|first3=Arnoldo|last4=Viljugrein|first4=Hildegunn|last5=Jansen|first5=Peder A.|date=January 2010|title=A stochastic model for the assessment of the transmission pathways of heart and skeleton muscle inflammation, pancreas disease and infectious salmon anaemia in marine fish farms in Norway|journal=Preventive Veterinary Medicine|volume=93|issue=1|pages=51–61|doi=10.1016/j.prevetmed.2009.09.010|pmid=19811843|issn=0167-5877}}</ref>

In 2014, Martinez-Rubio et al. conducted a study in which cardiomyopathy syndrome (CMS), a severe cardiac disease in Atlantic salmon (''Salmo salar''), was investigated pertaining the effects of functional feeds with reduced lipid content and increased eicosapentaenoic acid levels in controlling CMS in salmon after infection with piscine myocarditis virus (PMCV). Functional feeds are defined as high-quality feeds that beyond purposes of nutrition, they are formulated with health promoting features that could be beneficial in supporting disease resistance, such as CMS. Choosing a clinical nutrition approach using functional feeds could potentially move away from [[Chemotherapy|chemotherapeutic]] and [[antibiotic]] treatments, which could lower the costs of disease treatment and management in fish farms. In this investigation three fishmeal-based diets were served—one made of 31% lipid and the other two made of 18% lipid (one contained fishmeal and the other krill meal. Results demonstrated a significant difference in the immune and inflammatory responses and pathology in heart tissue as the fish were infected with PMCV. Fish fed with functional feeds with low lipid content demonstrated milder and delayed inflammatory response and therefore, less severe heart lesions at earlier and later stages after PMCV infection.<ref>{{Cite journal|last1=Martinez-Rubio|first1=Laura|last2=Evensen|first2=Øystein|last3=Krasnov|first3=Aleksei|last4=Jørgensen|first4=Sven|last5=Wadsworth|first5=Simon|last6=Ruohonen|first6=Kari|last7=Vecino|first7=Jose LG|last8=Tocher|first8=Douglas R|date=2014|title=Effects of functional feeds on the lipid composition, transcriptomic responses and pathology in heart of Atlantic salmon (Salmo salar L.) before and after experimental challenge with Piscine Myocarditis Virus (PMCV)|journal=BMC Genomics|volume=15|issue=1|pages=462|doi=10.1186/1471-2164-15-462|pmid=24919788|issn=1471-2164|pmc=4079957 |doi-access=free }}</ref>

=== Stocking density ===
Secondly, farmed fish are kept in concentrations never seen in the wild (e.g. 50,000 fish in a {{convert|2|acre|m2|adj=on}} area.<ref>{{cite web|url=http://www.gi.alaska.edu/ScienceForum/ASF9/984.html|title=Fuss over Farming Fish, Alaska Science Forum|access-date=30 January 2016|archive-url=https://web.archive.org/web/20120419072032/http://www2.gi.alaska.edu/ScienceForum/ASF9/984.html|archive-date=2012-04-19|url-status=dead}}</ref>). However, fish tend also to be animals that aggregate into large schools at high density. Most successful aquaculture species are schooling species, which do not have social problems at high density. Aquaculturists feel that operating a rearing system above its design capacity or above the social density limit of the fish will result in decreased growth rate and increased [[feed conversion ratio]] (kg dry feed/kg of fish produced), which results in increased cost and risk of health problems along with a decrease in profits. Stressing the animals is not desirable, but the concept of and measurement of stress must be viewed from the perspective of the animal using the scientific method.<ref>{{cite journal | year = 2006 | title = Current issues in fish welfare| url = http://curis.ku.dk/ws/files/22567895/Review_paper__Current_issues_in_fish_welfare.pdf| journal = Journal of Fish Biology | volume = 68 | issue = 2| pages = 332–372 | doi=10.1111/j.0022-1112.2006.001046.x| last1 = Huntingford| first1 = F. A| last2 = Adams| first2 = C| last3 = Braithwaite| first3 = V. A| last4 = Kadri| first4 = S| last5 = Pottinger| first5 = T. G| last6 = Sandoe| first6 = P| last7 = Turnbull| first7 = J. F| bibcode = 2006JFBio..68..332H| s2cid = 84511123}}</ref>

=== Parasites and disease ===
[[Sea lice]], particularly ''Lepeophtheirus salmonis'' and various ''Caligus'' species, including ''C. clemensi'' and ''C. rogercresseyi'', can cause deadly infestations of both farm-grown and wild salmon.<ref>[https://web.archive.org/web/20101214173552/http://farmedanddangerous.org/uploads/File/Reports/SeaLice_FullReport.pdf Sea Lice and Salmon: Elevating the dialogue on the farmed-wild salmon story] ''Watershed Watch Salmon Society'', 2004.<!--accessed January 15, 2010--></ref><ref>{{cite journal | last1 = Bravo | first1 = S | year = 2003 | title = Sea lice in Chilean salmon farms | journal = Bull. Eur. Assoc. Fish Pathol | volume = 23 | pages = 197–200 }}</ref> Sea lice are [[ectoparasite]]s which feed on mucus, blood, and skin, and migrate and latch onto the skin of wild salmon during free-swimming, planktonic ''nauplii'' and ''copepodid'' larval stages, which can persist for several days.<ref>{{cite journal | last1 = Morton | first1 = A. | last2 = Routledge | first2 = R. | last3 = Peet | first3 = C. | last4 = Ladwig | first4 = A. | year = 2004 | title = Sea lice (Lepeophtheirus salmonis) infection rates on juvenile pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon in the nearshore marine environment of British Columbia, Canada | journal = Canadian Journal of Fisheries and Aquatic Sciences | volume = 61 | issue = 2| pages = 147–157 | doi=10.1139/f04-016}}</ref><ref>Peet, C. R. 2007. Interactions between sea lice (''Lepeophtheirus salmonis'' and ''Caligus clemensi'') and juvenile chum (''Oncorhynchus keta'') and pink salmon (''Oncorhynchus gorbuscha'') in British Columbia. M. Sc. Thesis, University of Victoria.</ref><ref>{{cite journal | last1 = Krkošek | first1 = M. | last2 = Gottesfeld | first2 = A. | last3 = Proctor | first3 = B. | last4 = Rolston | first4 = D. | last5 = Carr-Harris | first5 = C. | last6 = Lewis | first6 = M.A. | year = 2007 | title = Effects of host migration, diversity, and aquaculture on disease threats to wild fish populations | journal = Proceedings of the Royal Society of London, Series B | volume = 274 | issue = 1629| pages = 3141–3149 | doi=10.1098/rspb.2007.1122 | pmid=17939989 | pmc=2293942}}</ref> Large numbers of highly populated, open-net salmon farms can create exceptionally large concentrations of sea lice; when exposed in river estuaries containing large numbers of open-net farms, many young wild salmon are infected, and do not survive as a result.<ref>{{cite journal | last1 = Morton | first1 = A. | last2 = Routledge | first2 = R. | last3 = Krkošek | first3 = M. | year = 2008 | title = Sea louse infestation in wild juvenile salmon and Pacific herring associated with fish farms off the east-central coast of Vancouver Island, British Columbia | journal = North American Journal of Fisheries Management | volume = 28 | issue = 2| pages = 523–532 | doi=10.1577/m07-042.1| bibcode = 2008NAJFM..28..523M }}</ref><ref>{{cite journal | last1 = Krkošek | first1 = M. | last2 = Lewis | first2 = M.A. | last3 = Morton | first3 = A. | last4 = Frazer | first4 = L.N. | last5 = Volpe | first5 = J.P. | year = 2006 | title = Epizootics of wild fish induced by farm fish | journal = Proceedings of the National Academy of Sciences | volume = 103 | issue = 42| pages = 15506–15510 | doi=10.1073/pnas.0603525103 | pmid=17021017 | pmc=1591297| bibcode = 2006PNAS..10315506K | doi-access = free }}</ref> Adult salmon may survive otherwise critical numbers of sea lice, but small, thin-skinned juvenile salmon migrating to sea are highly vulnerable. On the [[Pacific coast of Canada]], the louse-induced mortality of pink salmon in some regions is commonly over 80%.<ref>{{cite journal | last1 = Krkošek | first1 = Martin | display-authors = etal | year = 2007 | title = Report: "Declining Wild Salmon Populations in Relation to Parasites from Farm Salmon | journal = Science | volume = 318 | issue = 5857| pages = 1772–1775 | doi=10.1126/science.1148744 | pmid=18079401| bibcode = 2007Sci...318.1772K | s2cid = 86544687 }}</ref> In Scotland, official figures show that more than nine million fish were lost to disease, parasites, botched treatment attempts and other problems on fish farms between 2016 and 2019.<ref name="The Ferret">{{Citation |last=Edwards |first=Rob |date=2019-04-14 |title=Mass deaths: nine million fish killed by diseases at Scottish salmon farms |journal=[[The Ferret (website)|The Ferret]] |url=https://theferret.scot/salmon-deaths-farms-nine-million/ |access-date=2019-06-15 |postscript=.}}</ref> One of the treatments for parasite infestations involved bathing fish in hydrogen peroxide,<ref>{{Cite web|title=Use of Hydrogen Peroxide in Finfish Aquaculture|url=https://thefishsite.com/articles/use-of-hydrogen-peroxide-in-finfish-aquaculture|access-date=2021-11-14|website=thefishsite.com|date=13 February 2009 |language=en}}</ref> which can harm or kill farmed fish if they are in a weak condition or if the chemical concentration is too strong.

A 2008 meta-analysis of available data shows that salmon farming reduces the survival of associated wild salmon populations. This relationship has been shown to hold for Atlantic, steelhead, pink, chum, and coho salmon. The decrease in survival or abundance often exceeds 50%.<ref>{{cite journal | last1 = Ford | first1 = JS | last2 = Myers | first2 = RA | year = 2008 | title = A Global Assessment of Salmon Aquaculture Impacts on Wild Salmonids| journal = PLOS Biol | volume = 6 | issue = 2| page = e33 | doi=10.1371/journal.pbio.0060033 | pmid=18271629 | pmc=2235905 | doi-access = free }}</ref>

[[Fish diseases and parasites|Diseases and parasites]] are the most commonly cited reasons for such decreases. Some species of sea lice have been noted to target farmed coho and Atlantic salmon.<ref>{{cite web|url=http://www.umaine.edu/livestock/Publications/sea_lice_bullets.htm|archive-url=https://web.archive.org/web/20100521115210/http://www.umaine.edu/livestock/Publications/sea_lice_bullets.htm|url-status=dead|archive-date=2010-05-21|title=Sea Lice Information Bullets}}</ref> Such parasites have been shown to have an effect on nearby wild fish. One place that has garnered international media attention is British Columbia's [[Broughton Archipelago]]. There, juvenile wild salmon must "run a gauntlet" of large fish farms located off-shore near river outlets before making their way to sea. The farms allegedly cause such severe sea lice infestations that one study predicted in 2007 a 99% collapse in the wild salmon population by 2011.<ref>{{cite web|title=Fish Farms Drive Wild Salmon Populations Toward Extinction|url=https://www.sciencedaily.com/releases/2007/12/071213152606.htm|website=ScienceDaily|access-date=2018-01-06|date=16 December 2007}}</ref> This claim, however, has been criticized by numerous scientists who question the correlation between increased fish farming and increases in sea lice infestation among wild salmon.<ref>{{cite web|url=http://www.newsdata.com/fishletter/242/4story.html|title=Northwest Fishletter|access-date=30 January 2016}}</ref>

Because of parasite problems, some aquaculture operators frequently use strong antibiotic drugs to keep the fish alive, but many fish still die prematurely at rates up to 30%.<ref>Lymbery, P. CIWF Trust report, "[http://www.eurocbc.org/fz_lymbery.pdf In Too Deep – The Welfare of Intensively Farmed Fish]" (2002)</ref> Additionally, other common drugs used in salmonid fish farms in North America and Europe include anesthetic, chemotherapeutic, and anthelmintic agents.<ref>{{Cite journal|last1=Burka|first1=J. F.|last2=Hammell|first2=K. L.|last3=Horsberg|first3=T. E.|last4=Johnson|first4=G. R.|last5=Rainnie|first5=D. J.|last6=Speare|first6=D. J.|date=October 1997|title=Drugs in salmonid aquaculture – A review|journal=Journal of Veterinary Pharmacology and Therapeutics|volume=20|issue=5|pages=333–349|doi=10.1046/j.1365-2885.1997.00094.x|pmid=9350253|issn=0140-7783}}</ref> In some cases, these drugs have entered the environment.<ref>{{Cite journal|last1=Cabello|first1=Felipe C.|last2=Godfrey|first2=Henry P.|last3=Tomova|first3=Alexandra|last4=Ivanova|first4=Larisa|last5=Dölz|first5=Humberto|last6=Millanao|first6=Ana|last7=Buschmann|first7=Alejandro H.|date=2013-05-26|title=Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health|journal=Environmental Microbiology|volume=15|issue=7|pages=1917–1942|doi=10.1111/1462-2920.12134|pmid=23711078|issn=1462-2912|doi-access=free|bibcode=2013EnvMi..15.1917C }}</ref> Additionally, the residual presence of these drugs in human food products has become controversial. Use of antibiotics in food production is thought to increase the prevalence of [[antibiotic resistance]] in human diseases.<ref>{{cite web|url=https://www.fda.gov/oc/opacom/hottopics/antiresist_facts.html|title=Public Health Focus|website=[[Food and Drug Administration]]}}</ref> At some facilities, the use of antibiotic drugs in aquaculture has decreased considerably due to vaccinations and other techniques.<ref>{{cite web|url=http://www.ooa.unh.edu/environment/environment_care.html|archive-url=https://web.archive.org/web/20090810082202/http://www.ooa.unh.edu/environment/environment_care.html|url-status=dead|archive-date=2009-08-10|date=2007 |title=Fish care|author=Atlantic Marine Aquaculture Center|publisher=University of New Hampshire}}</ref> However, most fish-farming operations still use antibiotics, many of which escape into the surrounding environment.<ref>{{cite news|url=https://www.nytimes.com/2009/07/27/world/americas/27salmon.html| title=Chile's Antibiotics Use on Salmon Farms Dwarfs That of a Top Rival's |date=July 26, 2009|access-date=2009-08-28 | work=The New York Times | first=Alexei | last=Barrionuevo}}</ref>

The lice and pathogen problems of the 1990s facilitated the development of current treatment methods for sea lice and pathogens, which reduced the stress from parasite/pathogen problems. However, being in an ocean environment, the transfer of disease organisms from the wild fish to the aquaculture fish is an ever-present risk.<ref>{{cite journal | year = 2002 | title =Trends in therapy and prophylaxis 1991–2001 | url =https://eafp.org/download/2002-Volume22/Issue%202/22_117.pdf | journal = Bulletin of the European Association of Fish Pathologists | volume = 22 | issue = 2| pages = 117–125 }}</ref>
[[File:Criadero de peces en el Lago Titicaca cerca de Copacabana Bolivia.jpg|thumb|A [[Lake trout|North American lake trout]] fishing farm on [[Lake Titicaca]] near [[Copacabana, Bolivia|Copacabana]], [[Bolivia]]. Since their introduction in the 1930s, trout have been an [[invasive species]] endangering the local fish population.<ref>{{Cite web |last1=Magazine |first1=Smithsonian |last2=Bloudoff-Indelicato |first2=Mollie |title=What Are North American Trout Doing in Lake Titicaca? |url=https://www.smithsonianmag.com/science-nature/what-are-north-american-trout-doing-lake-titicaca-180957472/ |access-date=2023-07-24 |website=Smithsonian Magazine |language=en}}</ref>]]

=== Ecosystem impacts ===
The large number of fish kept long-term in a single location contributes to [[habitat destruction]] of the nearby areas.<ref>{{cite journal|last1=Naylor|first1=RL|last2=Goldburg|first2=RJ|last3=Mooney|first3=H|display-authors=etal|year=1998|title=Nature's Subsidies to Shrimp and Salmon Farming|journal=Science|volume=282|issue=5390|pages=883–884|bibcode=1998Sci...282..883N|doi=10.1126/science.282.5390.883|s2cid=129814837}}</ref> The high concentrations of fish produce a significant amount of condensed faeces, often contaminated with drugs, which again affects local waterways.

Aquaculture not only impacts the fish on the farm, but it also influences other species, which in return are attracted to or repelled by the farms.<ref name=":0" /> Mobile fauna, such as crustaceans, fish, birds, and marine mammals, interact with the process of aquaculture, but the long-term or ecological effects as a result of these interactions is still unknown. Some of these fauna may be attracted or demonstrate repulsion.<ref name=":0">{{Cite journal|last1=Callier|first1=Myriam D.|last2=Byron|first2=Carrie J.|last3=Bengtson|first3=David A.|last4=Cranford|first4=Peter J.|last5=Cross|first5=Stephen F.|last6=Focken|first6=Ulfert|last7=Jansen|first7=Henrice M.|last8=Kamermans|first8=Pauline|last9=Kiessling|first9=Anders|date=2017-09-19|title=Attraction and repulsion of mobile wild organisms to finfish and shellfish aquaculture: a review|journal=Reviews in Aquaculture|volume=10|issue=4|pages=924–949|doi=10.1111/raq.12208|issn=1753-5123|url=https://archimer.ifremer.fr/doc/00406/51737/52435.pdf|doi-access=free}}</ref> The attraction/repulsion mechanism has various direct and indirect effects on wild organisms at individual and population levels. The interactions that wild organisms have with aquaculture may have implications on the management of fisheries species and the ecosystem in relation to how the fish farms are structured and organized.<ref name=":0" /> 

=== Siting ===
If aquaculture farms are placed in an area with strong current, pollutants can be flushed out of the area fairly quickly.<ref>{{Cite web |title=Plenty of Fish on the Farm |url=https://thebreakthrough.org/articles/plenty-of-fish-on-the-farm |access-date=2025-05-14 |website=The Breakthrough Institute |language=en}}</ref><ref>{{Cite web |date=2016-04-13 |title=Making Fish Farming More Sustainable – State of the Planet |url=https://news.climate.columbia.edu/2016/04/13/making-fish-farming-more-sustainable/ |access-date=2025-05-14 |language=en-US}}</ref> This helps manage the pollution problem and also aids in overall fish growth.
Concern remains that resultant bacterial growth fertilised by fish faeces strips the water of oxygen, reducing or killing off the local marine life. Once an area has been so contaminated, fish farms are typically moved to new, uncontaminated areas. This practice has angered nearby fishermen.<ref name="nyt1">{{cite news|url=https://www.nytimes.com/2008/03/27/world/americas/27salmon.html|title=Salmon Virus Indicts Chile's Fishing Methods|author=The New York Times|work=Nyt|date=27 March 2008|access-date=27 March 2008}}</ref>

Other potential problems faced by aquaculturists include the obtaining of various permits and water-use rights, profitability, concerns about [[invasive species]] and [[genetic engineering]] depending on what species are involved, and interaction with the [[United Nations Convention on the Law of the Sea]].

=== Genetic engineering ===
In regards to [[genetically engineered salmon|genetically engineered, farmed salmon]], concern has been raised over their proven reproductive advantage and how it could potentially decimate local fish populations, if released into the wild. Biologist Rick Howard did a controlled laboratory study where wild fish and [[genetically engineered fish]] were allowed to breed.<ref>{{cite web|url=http://news.uns.purdue.edu/html4ever/2004/040223.Howard.transgenic.html|title=Purdue scientists: Genetically modified fish could damage ecology|access-date=30 January 2016}}</ref> In 1989, [[AquaBounty Technologies]] developed the [[AquAdvantage salmon]]. The concerns and critiques of cultivating this genetically engineered fish in aquaculture are that the fish will escape and interact with other fish ultimately leading to the reproduction with other fishes. However, the FDA, has determined that while net pens would not be the most appropriate to prevent escapes, raising the salmon in Panama waters would effectively prevent escape because the water conditions there would fail to support long-term survival of any escaped salmon.<ref name=":1" /> Another method of preventing Aqua Advantage fish from impacting the ecosystems in the case they escape suggested by the FDA was to create sterile triploid females. This way concerns on reproducing with other fishes would be out of the question.<ref name=":1">{{Cite journal|last=Medicine|first=Center for Veterinary|date=2019-04-12|title=AquAdvantage Salmon - Response to Public Comments on the Environmental Assessment|url=https://www.fda.gov/animal-veterinary/animals-intentional-genomic-alterations/aquadvantage-salmon-response-public-comments-environmental-assessment|journal=FDA}}</ref> The genetically engineered fish crowded out the wild fish in spawning beds, but the offspring were less likely to survive. The colorant used to make pen-raised salmon appear rosy like the wild fish has been linked with retinal problems in humans.<ref name="nyt1"/>

=== Labeling ===
In 2005, Alaska passed legislation requiring that any genetically altered fish sold in the state be labeled.<ref>{{cite act |title= Relating to labeling and identification of genetically modified fish and fish products|type= Alaskan Senate Bill |number= 25|date= 19 May 2005|url= http://www.akleg.gov/basis/Bill/Text/24?Hsid=SB0025Z|access-date= 2 December 2017}}</ref>
In 2006, a ''[[Consumer Reports]]'' investigation revealed that farm-raised salmon is frequently sold as wild.<ref>{{cite web|url=http://www.chathamjournal.com/weekly/living/food/cr-salmon-wild-60705.shtml| title=Consumer Reports reveals that farm-raised salmon is often sold as "wild"| date = July 5, 2006| access-date= 29 June 2010}}</ref>

In 2008, the US [[National Organic Standards Board]] allowed farmed fish to be labeled as organic provided less than 25% of their feed came from wild fish. This decision was criticized by the advocacy group [[Food & Water Watch]] as "bending the rules" about organic labeling.<ref>{{cite news| url=https://www.washingtonpost.com/wp-dyn/content/article/2008/11/19/AR2008111903787.html |title= USDA Panel Approves First Rules For Labeling Farmed Fish 'Organic'| date= November 20, 2008| access-date= 29 June 2010 | newspaper=The Washington Post | first1=Juliet | last1=Eilperin | first2=Jane | last2=Black}}</ref> In the European Union, fish labeling as to species, method of production and origin has been required since 2002.<ref name="fishonline1">{{cite web|url=http://www.fishonline.org/buying_eating/labelling.php#link4 |title=Environmental Labelling |access-date=29 June 2010 |url-status=dead |archive-url=https://web.archive.org/web/20100325233840/http://www.fishonline.org/buying_eating/labelling.php#link4 |archive-date=March 25, 2010 }}</ref>

Concerns continue over the labeling of salmon as farmed or wild-caught, as well as about the humane treatment of farmed fish. The [[Marine Stewardship Council]] has established an Eco label to distinguish between farmed and wild-caught salmon,<ref>{{cite web| url=http://www.msc.org/newsroom/news/msc-eco-label-helps-consumers-identify-certified| title= MSC eco-label helps consumers identify certified wild Alaska salmon| date =January 15, 2004| access-date= 29 June 2010}}</ref> while the [[RSPCA]] has established the Freedom Food label to indicate humane treatment of farmed salmon, as well as other food products.<ref name="fishonline1"/>