Integrated recycling systems

One of the largest problems with freshwater aquaculture is that it can use a million gallons of water per acre (about 1 m³ of water per m²) each year. Extended water purification systems allow for the reuse (recycling) of local water.

The largest-scale pure fish farms use a system derived (admittedly much refined) from the New Alchemists in the 1970s. Basically, large plastic fish tanks are placed in a greenhouse. A hydroponic bed is placed near, above or between them. When tilapia are raised in the tanks, they are able to eat algae, which naturally grows in the tanks when the tanks are properly fertilized.

The tank water is slowly circulated to the hydroponic beds where the tilapia waste feeds a commercial plant crops. Carefully cultured microorganisms in the hydroponic bed convert ammonia to nitrates, and the plants are fertilized by the nitrates and phosphates. Other wastes are strained out by the hydroponic media, which doubles as an aerated pebble-bed filter.

This system, properly tuned, produces more edible protein per unit area than any other. A wide variety of plants can grow well in the hydroponic beds. Most growers concentrate on herbs (e.g. parsley and basil), which command premium prices in small quantities all year long. The most common customers are restaurant wholesalers.

Since the system lives in a greenhouse, it adapts to almost all temperate climates, and may also adapt to tropical climates. The main environmental impact is discharge of water that must be salted to maintain the fishes' electrolyte balance. Current growers use a variety of proprietary tricks to keep fish healthy, reducing their expenses for salt and waste water discharge permits. Some veterinary authorities speculate that ultraviolet ozone disinfectant systems (widely used for ornamental fish) may play a prominent part in keeping the Tilapia healthy with recirculated water.

A number of large, well-capitalized ventures in this area have failed. Managing both the biology and markets is complicated.

Irrigation ditch or pond systems

These use irrigation ditches or farm ponds to raise fish. The basic requirement is to have a ditch or pond that retains water, possibly with an above-ground irrigation system (many irrigation systems use buried pipes with headers.) Using this method, one can store one's water allotment in ponds or ditches, usually lined with bentonite clay. In small systems the fish are often fed commercial fish food, and their waste products can help fertilize the fields. In larger ponds, the pond grows water plants and algae as fish food. Some of the most successful ponds grow introduced strains of plants, as well as introduced strains of fish.

Control of water quality is crucial. Fertilizing, clarifying and pH control of the water can increase yields substantially, as long as eutrophication is prevented and oxygen levels stay high.Yields can be low if the fish grow ill from electrolyte stress.

Cage system

Fish cages are placed in lakes, bayous, ponds, rivers or oceans to contain and protect fish until they can be harvested. They can be constructed of a wide variety of components. Fish are stocked in cages, artificially fed, and harvested when they reach market size. A few advantages of fish farming with cages are that many types of waters can be used (rivers, lakes, filled quarries, etc.), many types of fish can be raised, and fish farming can co-exist with sport fishing and other water uses. Cage farming of fishes in open seas is also gaining popularity. Concerns of disease, poaching, poor water quality, etc., lead some to believe that in general, pond systems are easier to manage and simpler to start. Also, past occurrences of cage-failures leading to escapes, have raised concern regarding the culture of non-native fish species in open-water cages. Even though the cage-industry has made numerous technological advances in cage construction in recent years, the concern for escapes remains valid.

Classic fry farming

Trout and other sport fish are often raised from eggs to fry or fingerlings and then trucked to streams and released. Normally, the fry are raised in long, shallow concrete tanks, fed with fresh stream water. The fry receive commercial fish food in pellets. While not as efficient as the New Alchemists' method, it is also far simpler, and has been used for many years to stock streams with sport fish. European eel (Anguilla anguilla) aquaculturalists procure a limited supply of glass eels, juvenile stages of the European eel which swim north from the Sargasso Sea breeding grounds, for their farms. The European eel is threatened with extinction because of the excessive catch of glass eels by Spanish fishermen and overfishing of adult eels in, e.g., the Dutch IJsselmeer, Netherlands. As per 2005, no one has managed to breed the European eel in captivity.

The issue of feeds in fish farming has been a controversial one. Many cultured fishes (tilapia, carp, catfish, many others) require no meat or fish products in their diets. Top-level carnivores (most salmon species) depend on fish feed of which a 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.

Secondly, farmed fish are kept in concentrations never seen in the wild (e.g. 50,000 fish in a 2-acre (8,100 m²) area.) with each fish occupying less room than the average bathtub. This can cause several forms of pollution. Packed tightly, fish rub against each other and the sides of their cages, damaging their fins and tails and becoming sickened with various diseases and infections.

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 tend to 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 FCR (food conversion ratio - kg dry feed/kg of fish produced), which will result 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.

Some species of sea lice have been noted to target farmed coho and Atlantic salmon. 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. It is alleged that the farms cause such severe sea lice infestations that one study predicted a 99% collapse in the wild salmon population in another four years. 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.

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 of up to 30 percent). In some cases, these drugs have entered the environment. 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. At some facilities, the use of antibiotic drugs in aquaculture has decreased considerably due to vaccinations and other techniques. However, most fish farming operations still use antibiotics, many of which escape into the surrounding environment.

The lice and pathogen problems of the 1990s facilitated the development of current treatment methods for sea lice and pathogens. These developments 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.

The very large number of fish kept long-term in a single location contributes to habitat destruction of the nearby areas. The high concentrations of fish produce a significant amount of condensed faeces, often contaminated with drugs, which again affect local waterways. However, these effects are very local to the actual fish farm site and are minimal to non-measurable in high current sites.

Other potential problems faced by aquaculturists are 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.