According to reports in the journal Science, however, farmed salmon may contain high levels of dioxins. Toxic PCB (polychlorinated biphenyl) levels may be up to eight times higher in farmed salmon than in wild salmon. Omega-3 content may also be lower than in wild caught specimens, and in a different proportion to what is found naturally.

According to a 2006 study published in the Journal of the American Medical Association, the benefits of eating even farmed salmon still outweigh any risks imposed by contaminants.

The population of wild salmons declined markedly in recent decades, especially north Atlantic populations which spawn in the waters of western Europe and eastern Canada, and wild salmon in the Snake and Columbia River system in northwestern United States. The decline is attributed, among others, to the following factors:

• Disease transfer from open net cage salmon farming, especially sea lice. The European Commission (2002) concluded “The reduction of wild salmonid abundance is also linked to other factors but there is more and more scientific evidence establishing a direct link between the number of lice-infested wild fish and the presence of cages in the same estuary.”[12] It is reported that wild salmon on the west coast of Canada are being driven to extinction by sea lice from nearby salmon farms.
• Loss of invertebrate diversity and population density in rivers because of modern farming methods and various sources of pollution, thus reducing food availability.

Source: Wikipedia (All text is available under the terms of the GNU Free Documentation License)

For more information (background, pictures, experiments and references): Salmon, Fish Farm