To add to liha's nice write-up detailing some of the downsides to aquaculture, the following information should also be considered.

In many circumstances, the species being farmed are saltwater species, meaning that estuary or wetland production, as suggested above, is not a possibility. Under those circumstances, coastal areas are penned-off, and production occurs therein. There are two major problems with this approach. First, these coastal areas are among the most important nursery areas for many marine fish species, and massive aquaculture installations can inadvertintly devastate wild fish populations as a result. Second, the water in these nearshore areas is often considerably warmer than that found in the species native habitat. While this increases growth rates, which is helpful for the producers, it also stresses the animals physiologically and increases susceptibility to disease and parisitism. Further, one thing rarely mentioned when discussing the relative merits of aquaculture is the production of food for the farmed animals. Aquaculture is often mentioned as a wonderful solution to the depletion of the ocean, and as an economically viable manner to produce the fish and shellfish desired by humans without hurting native stocks. However, the production of fish pellets is, in and of itself, highly damaging to the environment. Huge seines, with very fine mesh, are used in the ocean to collect both invertebrates and fish larvae which are later dried and turned into pellets. This has two negative effects on native species. First, many of their young are destroyed in this manner, putting pressure on often already vulnerable stocks. Second, the invertebrates gathered in this way are the principal food source for many of the wild fish species. Taking this biomass (read: energy) out of the food web in large quantities results in lower biomass of the wild fish species that are supposed to be conserved by aquaculture.

Many scientists who work in the field (fisheries science, oceanography, limnology) now believe that in many if not most circumstances, aquaculture can in fact have a greater environmental impact than directly fishing wild stocks.

Not only fish, but advancements in aquaculture in recent years are giving us mussels, crabs and other shellfish.

Aquaculture is the raising of water-residing livestock. This allows the taste and size of the yummy creatures in question to be controlled. In some cases (like mussels) the farmed variants are of higher quality (as a food) than the wild variety. (in the case of mussels you end up with a thinner shell and larger meat, catfish are not as "muddy" tasting and contain fewer parasites).

Aquaculture is also a boon to the environmentalist movement. Most aquacultural methods have minimal impact on the environment, and indeed aquaculture is being used to preserve the wild populations of certain species (such as salmon). Also, new architectual designs of breeding and holding tanks use up less land and resources than the raising of cattle or sheep.

Aquaculture is currently a growing industry but it will provide us with cheaper seafood (something I am all for).

If anyone can give me some downsides to aquaculture I'd love a "couterpoint" posted here
The downsides of requested by LordOmar:

Aquaculture takes place mostly in coastal wetlands in brackish water. Wetlands, which include salt marshes, mangrove swamps and mudflats, are more sheltered than coastlines and are excellent for aquaculture. Unfortunately, most wetlands are thought of as desolate, unproductive 'wastelands' and are threatened by development. The expansion of agriculture, industry, and urban areas leads to the removal of natural vegetation and land reclamation. Aquaculture also leads to the removal of natural vegetation in order for ponds to be dug. Once the ponds have been filled with water, excess nutrients and waste product are discharged into the pondwater which then infiltrates groundwater supplies and coastal areas. Eutrophication of the ponds is also possible due to the addition of nutrients.

There is also a possiblity of species mixing leading to a decrease in biodiversity. Please see the node on aquaculture escapees.

If aquaculture is to be successful, without causing damage to the natural environmet, there must be an understanding of how a particular ecosystem works allowing specific aquaculture methods to be developed.
Aquaculture is basically fish farming. It is a growing worldwide industry. There has been a 200% increase in the amount of aquaculture products produced every five years since 1985. Currently 30 million metric tons or about one third of all seafood product consumed worldwide is produced by aquaculture. The largest producer is China with about 50% of the total aquaculture production.

Species such as shrimp, tilapia, salmon, crayfish, catfish, trout, carp, mussels, clams, oysters, scallops, and algae's are all farmed. Approximately 98% of all Atlantic salmon currently being consumed comes from aquaculture operations in Canada, Chile, and Norway.

Aquaculture offers the only viable alternative to the continued depletion of the ocean. Unfortunately an aquaculture farm developed with little regard for the environment or neighboring farmers can lead to the destruction of the local environment. This has been a problem in many developing countries where aquaculture is seen as a chance for a better life.

China, Taiwan, Thailand, Ecuador and India have all had aquaculture failures that led to environmental damage, due to unsustainable development or improper management and the loss of millions of dollars. China and Taiwan have yet to fully recover from their aquaculture collapses.

Yet a good aquaculture farm can actually improve the local environment in many areas. The keys are sustainable production levels, every operation is different, and dependent on their resources and location. Sustainable stocking densities, feeds, aeration, pond-based recycling systems, closed recirculating systems, settling ponds, use of wetlands, integration with agriculture, minimal use of fertilizers, and biological filtration can all contribute to a sustainable aquaculture farm. An aquaculture farm can be part a sewage treatment plant, and can actually improve the yield of clean fresh water.

Settling ponds using plants such as duckweed and water hyacinths can reduce high levels of ammonia and phosphorus in water, which can then sustain clams and oysters, algae's such as Gracilaria and fish like tilapia and carp. And after purifying the water for the fish, (or other aquaculture product), the excess plants can then be eaten by the aquaculture product. Incorporating a settling pond, into an aquaculture pond decreases water use, (via recycling), reduces pollution, decreases costs and improves yields.

Duckweed is up to 45% protein, and has high concentrations of the essential amino acids lysine and methionine and is also high in trace minerals and pigments. Fresh duckweed can be fed directly to tilapia. Tilapia is a very fast growing fish and can reach two pounds in six to nine months. It produces a mild, soft, white fish fillet, with a slightly sweet taste. It is lean, tender, and reminds me of flounder or sole. Tilapia are vegetarian and thus can be co grown with shrimp.

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