Farm salmon are held in flow through nets and cages which allow fish waste and excess feed to freely pass into marine waters. These wastes frequently accumulate under salmon farms and may degrade the habitat surrounding the farm.

Many different compounds and chemicals are used in industrial salmon farming operations. In an effort to keep farmed fish healthy, salmon farmers add drugs such as antibiotics and therapeutants to the salmon feed as needed. The chemical Slice is used to treat farmed salmon for sea lice infestations, but it may also affect non-target wild crustaceans such as crabs and may remain in the environment. Other chemicals such as antifoulants and disinfectants are also released into the environment by farms in an attempt to control unwanted organisms and diseases. Little is known about how these chemicals affect the marine ecosystems, however, one study investigating contaminants near BC salmon farms found that rockfish near salmon farms had elevated levels of mercury compared with rockfish found elsewhere.  Watershed Watch Executive Director, Craig Orr, was a co-author on the resulting paper Ecosystemic effects of salmon farming increase mercury contamination in wild fish, Environmental Science and Technology 40 (11), pp 3489–3493.

One solution that may minimize the problems associated with open-net cage salmon farming is closed containment technology which provides a barrier between farmed salmon and the marine ecosystem.