Parasites occur naturally in the wild, but confining large numbers of farmed salmon in open net-pens over long periods of time creates artificial environments for parasites like the sea louse to multiply and spread. Their eggs are dispersed by the currents and can travel freely into and out of net-pens. Many salmon farms are located in more sheltered areas of the coast that are important migration routes of wild salmon.

Open net-pen salmon farms are located in areas along the coast where they can take advantage of ocean currents to deliver oxygen to their fish and disperse their wastes -- all at no cost to the industry. But there are costs to the ocean from these operations that extend from the surface to the seabed. The waste products (faeces and feed) from the farmed salmon in the pens are released directly into the surrounding water and settle to the sea floor. These wastes can change the chemical make-up and biological diversity of the seabed around the pens.

Pathogens - whether viruses or bacteria – are micro-organisms that can cause disease outbreaks in animals and plants. All organisms cope with pathogens in their natural environment. The ocean also has its share of ‘bugs’ that affect animals in the marine environment. Open net-pen salmon farms hold large numbers of fish at high density over long periods of time upsetting the natural balance and creating the right conditions for pathogens to amplify, mutate and spread to wild species that may be in the vicinity.

By-catch is the accidental harvest of marine species other than target species being fished or farmed. Open net-cage fish farms catch wild fish that can swim into their nets and until recently it's been hard to know just how big the problem is. A recent court action spotlighted this issue and now salmon farmers in British Columbia are required to report all bycatch of wild species and to immediately return them to the ocean outside the pens in a manner that causes the least harm as a condition of their aquaculture licence.