There have been a lot of issues raised about farm-raised salmon. I've basically given up salmon as it is hard to find wild salmon or it is very expensive.
The best information I found concerning this is something called "Seafood Watch" provided by Monterey Bay Aquarium. They basically say to avoid any farm raised Salmon.
Salmon farmers may use pesticides and antibiotics to control outbreaks of disease among the fish. When consumers eat this fish, the residues from the chemicals may affect their health or interfere with medicines they’re taking. The Environmental Defense has issued a health advisory for Farmed salmon due to high levels of PCBs and dioxins. For more information, visit their Ocean's Alive web site.
Salmon are farmed in open pens and cages in coastal areas. Waste from most farms is released directly into the ocean. Parasites and diseases from farmed salmon can spread to wild fish swimming near the farms. And feeding farmed salmon actually uses more fish than it produces, which puts more pressure on wild populations. Farmed salmon generally uses three pounds of wild fish to grow one pound of farmed salmon.
Segments of the salmon farming industry are improving their practices but the environmental impact is still increasing because production has risen more than 400% in the last decade. In the market, there is currently no way to tell which salmon are coming from more-sustainable farms, so for now we ask you to avoid farmed salmon and choose wild-caught salmon instead.