To make fish oil, you need fish that are low enough in the food chain to not have many PCBs. Fish oil is usually made from the menhaden fish (aka the alewife fish), which used to be plentiful all around the Atlantic coastline of the US, feeding on algae. With all those fish turned into fish oil pellets, there are massive algae blooms, and the food chain's getting disrupted.

See http://www.ethicurean.com/2009/03/23/menhaden/ and http://motherjones.com/environment/2006/03/ill-take-menhaden