Fish farms are located in sheltered areas that are important habitats for cetaceans and other sea mammals. The areas used by these farms can occupy habitat ordinarily used by whales, dolphins and porpoises. Acoustic harassment devices that are used by fish farms to keep seals away may also keep cetaceans away from breeding, feeding or resting sites.

The aquaculture industry releases a variety of pollutants into marine environments, including butyltins used as anti-foulants on cages and fish waste.

Vast quantities of untreated waste collect underneath fish farm cages and form a dense concentration of decaying matter, choking the seabed and contaminating the water.

Since fish farms are located in sheltered areas, there is less movement of water to flush the wastes, resulting in an increase of sewage-related bacteria and viruses.

Fish farms have also been shown to contribute to the problem of fish lice, a disease that has a negative impact on the survival rate of juvenile salmon stocks, a food source for many cetaceans.