Since the sensational 1994 discovery of James Fort, the first permanent English settlement in the New World, excavations have revealed palisade walls and numerous buildings, along with remarkable clues about the Anglo-American culture that started with the landing of colonists on Virginia’s Jamestown Island in 1607.

But because much of the original fort is buried underneath a Confederate earthwork called Fort Pocahontas, these discoveries forced a painful historical and archaeological trade-off. To reveal James Fort, nearly half of Fort Pocahontas has been removed.

In the process, invaluable traces of America’s founding have been discovered right next to remains from the Civil War. “It’s probably the only place you would have a story like that,” says Colin Campbell, president of Colonial Williamsburg, citing the conjunction of two pivotal moments in U.S. history. “I think it’s absolutely fascinating.”

To some observers, the fate of Fort Pocahontas — a series of rolling, grassy mounds shaded by old cedar trees — is a vivid demonstration of the axiom “Archaeology is always destructive.” But William Kelso, chief archaeologist at Jamestown Rediscovery, which is doing the excavation, disagrees: “If properly excavated and recorded digitally in 3-D, as we did, it is no longer valid to say we destroy sites.”

The remains of James Fort and Fort Pocahontas lie on 22.5 acres owned by Preservation Virginia, a nonprofit organization. The remaining 1,500 acres of Jamestown Island belong to the National Park Service. James Fort itself originally enclosed 1.1 acres.

Senior staff archaeologists Dan Schmidt, left, and David Givens work at the site of the CIvil War fort. (Scott Neville/FOR THE WASHINGTON POST)

The archaeologists working for Preservation Virginia have excavated Fort Pocahontas with the same care they apply to James Fort, says team member Bly Straube: “We’ve removed it with shovels and trowels, recording everything using [graphic information system software], digging in a grid system where it’s all mapped in. We’re not just arbitrarily digging things up.”

As Fort Pocahontas gets steadily cut away, valuable insights have been gained into Civil War fortifications. Last year a bombproof — an underground, timber-lined room where soldiers could hide if they were bombarded — was uncovered. It’s one of the few that professional archaeologists have ever excavated. Well-preserved log supports and even Civil War sandbags were unearthed.

Fort Pocahontas was established in 1861 as Confederate for-

ces prepared to defend Richmond from possible naval assault during the opening months of the war. (It is not to be confused with an 1864 Union fort of the same name, farther up the James River.) Military engineers unknowingly placed Fort Pocahontas right atop the traces of James Fort, the location of which had long been forgotten. But the spot is ideal for fortifications, with commanding views of the James River.

The decision to remove much of Fort Pocahontas took into account the fact that troops never fired a shot in anger from it during the Civil War. Instead, Pocahontas was abandoned as Union forces advanced overland in May 1862. The fort did, however, play a part in the most famous naval duel of the Civil War, between the Union’s USS Monitor and the Confederates’ Merrimack (renamed CSS Virginia), the first battle ever between ironclad warships. Confederates used the fort’s cannons to test armor plates for the Virginia, blasting them with eight-inch shells from powerful Columbiad cannons.

Kelso has found fragments of such shells, along with hundreds of spikes that once affixed the plank floors of the gun emplacements. Virginia’s plates later survived a pounding from the Monitor’s guns during their fabled 1862 engagement in the nearby waters of Hampton Roads.

The construction of Fort Pocahontas — primarily by slaves — severely damaged the underground remains of the southern half of James Fort. To create the earthwork, the workers scraped off the top layers of soil at the site, often to a depth of several feet, then piled the dirt high to create a berm. This scraping annihilated, or at least scrambled, the near-surface traces of the 1607 settlement.

The slaves’ shovels were slicing into one of the most important sites in American history, where 104 pioneers planted the British flag permanently in the New World in May 1607 and quickly erected a triangular wooden fort. Led for a time by Capt. John Smith, the tiny settlement was decimated by disease and Indian attack, but it rebounded after supply ships arrived in 1610, just as the beleaguered survivors of the original company, giving up hope, had started to sail down the river for home. The marriage of settler John Rolfe to Pocahontas, daughter of the local chief, heralded a more stable period: Anglo-America was safely underway.

A historical illustration shows the Civil War fort on the edge of the Janes river; behind it is a church that was built in 1617. (Virginia Historical Society, Mss5.1.Sn237.1.Vol3_0234)

In 2010, Kelso discovered the 1608 church inside James Fort where Pocahontas wed Rolfe. The uppermost five feet of its foundations were missing — carted several yards away to build Fort Pocahontas.

In the process of building the Civil War fort, according to an account at that time, the slaves happened upon “curious relics” from the colonial settlement of 250 years earlier, including an iron elbow-piece, or vambrace, belonging to a 17th-century suit of armor. The vambrace was donated to the Virginia Historical Society in the late 19th century; it is now on display at Jamestown’s Archaearium, a new museum. The vambrace is much better preserved than recently excavated armor, which is all reduced to rust due to exposure to moisture over time.

For Kelso, the vambrace is proof that Jamestown should be subjected to intensive archaeology now, as he is doing, not later. “Burials and iron objects are going to be gone in the next 20 years,” he says, as deterioration of buried items inexorably advances.

Since 1994, Kelso and his co-workers have recovered 1.4 million artifacts from James Fort. To fund the work, he relies on grants and donations and some gate receipts from visitors. But, says Straube, “It’s been a struggle to keep going.” In 2010 a partnership was formed with Colonial Williamsburg, and public programming has been increased to lure more paying visitors.

The lumpy, undulating earthen walls of Fort Pocahontas have turned out to be chockablock with small artifacts highlighting everyday life in the 1600s. Among them are a paring knife found last summer and Elizabethan coins that might have jingled in Shakespeare’s pocket before a settler brought them to America. “Over the years we have screened every square inch of a huge volume of soil,” says team member David Givens. “All the best stuff was up in the Confederate fort.”

Although the building of Fort Pocahontas severely damaged the southern part of James Fort, it helped preserve the northern section. Its imposing berms of heavy soil dissuaded casual digging by amateur archaeologists or looters. “I’m absolutely amazed at how much of James Fort is left,” says Al Luckenbach, a Maryland expert on colonial excavations. “There were so many opportunities for later generations to ruin the site.”

Farming and urbanization have swept away many Civil War earthworks in the South, including three of 11 rebel forts that defended Williamsburg. As Petersburg expanded in the mid-20th century, some sizable forts from the city’s 1864-65 siege were flattened for shopping malls and houses. But the case of Fort Pocahontas is virtually unprecedented: the deliberate removal of a historic earthwork that had been preserved within a park.

Because the James Fort site is in private hands, Kelso has enjoyed considerable latitude compared with what he might have encountered on federal property, where archaeology is discouraged except in advance of necessary construction or roadwork. Kelso stresses that he has “met and exceeded” federal standards for investigating an archaeological site. Preservation Virginia’s initial decision to excavate was approved by an advisory committee of archaeologists.

James Lighthizer, president of the Civil War Trust, a preservation organization, regards the removal of Fort Pocahontas as an acceptable trade-off. “I would think James Fort would be a heck of a lot more important” than the 1861 earthwork on top, he says.

“The decision to dismantle the Confederate fort was taken with great care,” says Ivor Noel Hume, former director of archaeology for Colonial Williamsburg, who served on Preservation Virginia’s advisory panel. “And it was very carefully taken apart. They could have used a bulldozer. Instead, they have done as good a job as is possible to do.”

As one fort wanes, another is revealed in spectacular detail. “Destroying a Confederate fort to get to James Fort is a shame,” says Luckenbach. “But Virginia has lots of Confederate forts, but there’s only one James Fort. And it’s stunning what they’ve found there.”

Maynard is the author of five books, including “Princeton: America’s Campus,” an architectural history of America’s fourth-oldest university.