Fish farms are the water-based equivalents of land-based concentrated animal feeding operations, and as such they create the same, if not worse, environmental concerns.  One of the reasons farmed salmon contain higher levels of toxins than wild is because their feed is highly contaminated. A chemical of particular concern found in farmed salmon (but not in wild) is ethoxyquin - a rubber stabilizer, pesticide, preservative and antioxidant all in one, and a suspected carcinogen that damages DNA. Since the salmon pens are placed along wild salmon runs, they pose a severe threat to wild salmon that pass by, exposing wild fish to diseases such as piscine reovirus, which now threatens wild salmon with extinction.  Toxicology testing reveals farmed salmon is one of the most toxic foods in the world - more than five times more toxic than any other food tested, with eight times higher PCB levels than wild salmon. 

And farmed salmon isn't the only fish that you shouldn't eat. Others include: tilapia, Atlantic cod, Atlantic flatfish (Atlantic halibut, flounder, and sole), caviar, Chilean seabass, eel, imported basa, swai, or tra (often labeled as catfish), imported farmed shrimp, imported king crab, orange roughy, shark, Atlantic bluefin tuna, swordfish, king mackerel, goruper, or sturgeon. 

Yes, we're sad too. 

Here is the "Green List" of Monterey Bay Aquarium's Seafood Watch for healthier alternatives.