Penobscot Bay originates from the mouth of
Maine's
Penobscot River. 11,000 years ago, at the beginning of the
Holocene era, the
Gulf of Maine's sea level fell as low as 180 feet (55 m) below its present height. Penobscot Bay was then a continuation of Penobscot River that meandered through a broad lowland extending past present day Matinicus Island. Penobscot Bay is between
Muscongus Bay and
Blue Hill Bay.