APVA's director of archaeology William Kelso says the oyster shells in particular could reveal an environmental health report on the Chesapeake at the time the colonists arrived.
Already one fact seems obvious, Kelso says: The 17th-century oysters were doing quite well.
"These are very large and look really healthy," Kelso said. "They were growing really luxuriously.
"The thing that that tells you about is the salt content of the water. The more salt, the better they are."
By studying the oyster shells, scientists at the Virginia Institute of Marine Science in Gloucester Point will be able to establish a benchmark for how the bay has changed since Jamestown was founded, Kelso says.
The well was discovered at what had been the northernmost corner of the triangle-shaped fort that the colonists erected soon after they arrived in May 1607.
Smith, a figure most commonly linked to the legend of Pocahontas, was chosen to lead the colony in 1608. He immediately issued an edict that only those who worked would eat.
This harsh but effective order prompted the colonists to work harder to establish their foothold in the New World.
Smith later made a reference in his journal to a well that he ordered to be dug in 1608 or 1609.
Schmidt thinks the colonists built the well by first digging a large hole about ten feet (three meters) in diameter.
They gradually sank a long, square wooden shaft about six feet (two meters) wide on each side into the well and then backfilled around the shaft.
English miners commonly used this same technique in the 17th century.
Archaeologists have excavated about 14 feet (4 meters) below the ground's surface and think the well is perhaps 3 or 4 feet (1 or 1.2 meters) deeper.
Schmidt thinks the colonists may have used a ship's bilge pump to draw water from the well.
"It's absolutely possible that we will find a pump," Schmidt said. "That would be found at the bottom."
In October 1609 Smith was seriously injured in an accident and had to return to England for medical treatment. At about the same time, the well apparently became contaminated.
The colonists probably stopped using the well sometime after the winter of 1609-10, during which time hundreds of colonists died of starvation.
The well became a garbage pit until around 1618, when it was filled in and a house was built on the site. The house's fireplace and chimney sat atop the old well.
When the Civil War erupted in 1861, Union forces built an earthen fort on the site of the old Jamestown colony, covering the well in the process.
In the mid-1990s archaeologists discovered the outline of the original Jamestown fort and began excavating.
Discovering the well was a moment of delight for Kelso.
"I feel like it's as close as you can come to a time machine," he said. "It's an emotional and an intellectual exercise at the same time. It is exhilarating."
Kelso says summer interns have joined the work force and excavations will continue through August.
Willie Drye is author of Storm of the Century: The Labor Day hurricane of 1935, published by National Geographic Books.
Free Email News Updates
Sign up for our Inside National Geographic newsletter. Every two weeks we'll send you our top stories and pictures (see sample).
SOURCES AND RELATED WEB SITES