The Department of Marine Resources has closed upper Penobscot Bay to fishing after a court-ordered study found elevated concentrations of mercury in crab and lobster. Mercury pollution comes from lots of places, but this particular part of the Penobscot is a hotspot of contamination thanks to Holtrachem, a now-closed plant that made chlorine and other chemicals for the paper industry. In 2004 I wrote an article for Northern Sky News about Holtrachem (PDF), and the brave and diverse individuals who came together to stop the company from polluting waters here and abroad. It is a fascinating tale, and one that is not over with ongoing lawsuits over who is responsible for cleaning up the river and bay.
Maine Sea Grant also has a fact sheet about mercury in the Penobscot River Estuary (1.79 MB).