The problem is that modern life has contaminated many of the world's bodies of water, leaving the fish living there unsafe for human consumption. The main source of contamination that people are aware of in seafood is mercury, but that is only one concern. Many other toxins are common, including: flame retardants, PCBs, chlorinated dioxins, pesticides, oil, arsenic and melamine, just to name a few. These toxins are either present in the water in which the fish live, or in the food they are given.
Living in Ohio, there are many streams and lakes nearby for fishing, but after speaking with an ichthyologist at a local university who has tested toxicity, I don't feel safe eating anything that lives in them.* Since I try very hard to only eat local and ethically-raised meat sources, this leaves me with very few options.
But as the mother of a dairy-allergic child, I realize how important the calcium and vitamin D that seafood provides is for my son. His options for foods high in these two nutrients are more limited simply because he cannot drink milk.
I have found that the Environmental Defense Fund has some excellent resources for seafood safety.
Here is a complete list of Seafood Eco-Ratings. According to this chart, you shouldn't consume any of the following items due to high mercury or PCB content:
Chilean sea bass
All orange roughy
Yellow Perch from Lakes Huron and Ontario
All salmon (except wild Alaskan)
Imported wild sturgeon
Canned white/albacore tuna
Some people choose to take a fish oil supplement in order to get their nutrients. The Environmental Defense Fund also has a list of the safest supplements to take. Never take the following brands of fish oil:
To learn about the best sushi choices (both for your health and the environment) check out this list.
So it looks like for me and my family, with a very limited selection of seafood in the grocery store, our safest bet is to stick with wild Alaskan salmon, shrimp from Oregon, U.S. tilapia, and U.S. or Canada albacore tuna.
* Except for the fish from one river about 45 minutes away that he said had been tested as clean. This stream runs from a mountain at a high elevation and if you catch fish from higher up, they are less toxic. This ichthyologist said that is a good rule of thumb for eating fish that you have caught - the higher the elevation (so long as it is upstream from any potential pollution sources), the safer the fish.
Source - Environmental Defense Fund. http://www.edf.org/