A recent worldwide decline of ocean fishery stocks has stimulated rapid growth in cultivated production of fish and shellfish, usually known as fish farming. Between 1987 and 1997, for example, global fish production from farming doubled. Fish farming produces a quarter of all fish and shellfish eaten by humans, and, as global population increases, fish farming will probably become even more important in supplying human protein needs. Some experts even argue that in addition to helping to compensate for the decline in ocean harvests, fish farming will restore wild populations by relieving pressure on ocean fisheries. There is, however, little if any evidence that fish farming will restore ocean fishery stocks. The complexity of production systems leads to an underlying paradox: fish farming is a possible solution, but also a potential contributing factor, to the continued decline of ocean fishery stocks worldwide.

In the first place, the more intensive forms of fish farming, oriented toward high-volume production, threaten the sustainability of ocean fisheries through water pollution and ecological disruption. Intensive fish farming usually involves the enclosure of fish in a secure system; population densities are typically high, resulting in the generation of large amounts of waste and increased potential for the spread of pathogens. Habitat destruction through the spread of untreated waste, the escape of species not native to the farm's region, or contamination by new pathogens can all ensue, seriously damaging ocean and coastal resources and, ultimately, wild fishery stocks.

Even more important, intensive farming of many species of fish requires large inputs of fish meal and fish oil in order to supply fatty acids that vegetable matter lacks or essential amino acids that it inadequately supplies, like lysine and methionine. For the ten species of fish most commonly farmed, an average of 1.9 kilograms of wild fish is required for every kilogram of fish produced. Of the ten species, only three—catfish, milkfish, and carp—require less fish input than is eventually harvested, while the farming of carnivorous species like salmon has a very high input-to-output ratio. Although some defenders of fish farming contend that predatory carnivores in the wild consume even more fish than they would on a farm, farming of such carnivorous species requires up to 5 kilograms of wild fish for every kilogram of fish produced.

Expanding farm production does have the potential to alleviate some of the pressure on wild fishery stocks. For example, increasing the farm production of fish like salmon can reduce prices, deterring investment in fishing fleets and, over time, reducing fishing efforts. Similarly, other farmed fish like tilapia and channel catfish provide alternatives to ocean fish like cod and haddock. Nonetheless, even these benefits may in the end be lost because niche markets have started to develop for several species of wild-caught fish, causing their catch rates to remain high even as the production of viable farmed substitutes has increased.