Following publication of The History of Bristol and Bremen by John Johnston in 1873, serious interest in Pemaquid's settlements and succession of forts was awakened. John Henry Cartland did a more thorough investigation at the turn of the century, and was responsible for having Fort William Henry rebuilt in 1908, after the fort site was given to the State of Maine in 1902. Parts of the village and fort area were excavated (but not documented) in 1923 by archaeologist Warren King Moorehead, while on a futile search for evidence of Viking settlements.

In the mid-1960s, Helen Camp brought her methodical and scientific approach to the field where she had first noted a sizable depression beyond the Fort House, and modern archaeology began to discover Colonial Pemaquid. From the spring of 1965 until 1974, Camp and land owner Gordon Van Buskirk uncovered 14 foundations of buildings. In 1969, the Maine Bureau of Parks and Lands acquired the property, and from 1974 to 1980 Camp worked with Robert Bradley, state archaeologist, to excavate the officers' quarters of Fort William Henry and Fort Frederick.

Today's visitors can view cellar holes of 17th and 18th century structures, including dwellings, a forge, fortified warehouse and trading post, tavern, jail, and other buildings. During the summer months, a resident archaeologist is likely to be observed conducting digs to assess artifact-sensitive sites in conjunction with ongoing shoreline erosion studies.