Sea lice, particularly Lepeophtheirus salmonis and various Caligus species, including Caligus clemensi and Caligus rogercresseyi, can cause deadly infestations of both farm-grown and wild salmon. Sea lice are ectoparasites 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.

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. 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%.

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. 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.

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 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 feces, 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.

Concern remains that resultant bacterial growth strips the water of oxygen, reducing or killing off the local marine life. Once an area has been so contaminated, the fish farms are moved to new, uncontaminated areas. This practice has angered nearby fishermen.

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.