The levels in a clam chowder recipe vary depending on the specific recipe, but clams have the third-lowest mercury level of any fish studied by the U.S. Food and Drug Administration. Clams contain an average mercury level of 0.009 parts per million.
The Natural Resources Defense Council classifies clams as "Least Mercury," meaning they are safe to eat without restrictions for pregnant women. Clams are absent entirely from the Environmental Protection Agency's list of seafood with harmful levels of mercury. The Nutrition Experts blog states that clam chowder is safer than raw clams because the cooking process kills harmful organisms which may be present in raw shellfish.