Human occupation of the New England region of North America during the early Holocene has long been established archaeologically. However, the data exists almost solely from terrestrial sites. Vast portions of aerial land once available to early occupants of the area for resource procurement and living surfaces are now submerged. Underwater pre-Contact resources embedded in these submerged landforms will undeniably contribute to a holistic understanding of New England's cultural history. Examination of current archaeological procedures reveal that the archaeological standards, practices, and theories commonly employed in terrestrial archaeology are largely not being extended past the coastline into the underwater environment. This is due, in part, to the past history of professional skepticism regarding the preservation and accessibility of terrestrial archaeological deposits post-Holocene sea level rise. A report of global, submerged, terrestrial archaeology projects that show submerged, intact resources challenge this skepticism. A detailed review of an underwater survey in Boston Harbor, designed to predict, locate, and investigate submerged pre-Contact sites, is used as a case study to argue that these resources deserve the same rigorous study as terrestrial archaeological resources. Post-glacial deposition may act as an agent of preservation in New England waters, and past concerns of transgressive erosion are discussed in light of current geophysical research. Recommendations of how and why submerged pre-Contact archaeological resources should become commonplace within archaeological inquiry are supported by advances in technology, increased geophysical survey of the marine environment and knowledge of the prevailing laws governing archaeological resources underwater.