Investigative permits are issued for determining site suitability and monitoring the environment. All levels of government must be consistent with fisheries management issues such as public health and safety. Uneaten food and feces make up the bulk of waste discharge, which is localized within 30 m of the site. There is a concern about drugs being introduced into the ocean when fish in pens are treated. The antibiotics issued to fish should lose their effect after 30 days but information regarding this issue is poor.
Sites require permits that provide direction on good management practices.
Seals, sea lions and river otters are affected by salmon aquaculture. Salmon in net pens attract marine mammals and birds and this encounter can result in wounds, stress and mortalities of cultured fish. Methods of deterring predators such as the use of nets, dogs, night watches and scarecrows are not always effective. Trapping and underwater scaring devices are used, but require permits. Underwater acoustic devices have been known to disrupt communication in marine mammals by deafening them or scaring them away from the ecological area.