Based on his analysis of Jefferson's original edited manuscript pages of Notes on the State of Virginia, the historian Douglas Wilson argues that Jefferson undertook his investigation of the mound in 1784, a few years after he had begun drafting Notes. Jefferson was hardly the first American to disturb a burial mound; antiquarians had long sought artifacts, while farmers might have been interested only in leveling their fields. But Jefferson was the first American to conduct a scientific archaeological study. As such, his investigation was systematic, it set out to answer clear questions, and its findings were published.

Jefferson began his work by superficially digging in several areas of the mound. In each of these tests, he encountered bones from six inches to three feet below the surface, writing that they were arranged in "utmost confusion," or as if emptied from a basket and then covered with earth. Modern archaeologists describe this as a bundle secondary burial feature, meaning that Jefferson likely saw the remains of multiple individuals who were reburied from somewhere else. In fact, Jefferson estimated that the mound contained the remains of at least a thousand people. That number is large compared with other burial mounds in North America, but modern studies of similar mounds nearby support the number as reasonable. Jefferson also distinguished between the skulls of adults, children, and infants.

After these initial tests, Jefferson began his more-systematic fieldwork. Although he used the first-person in his writing about the dig, the scale of the excavation suggests that others were involved, presumably slaves from his Monticello plantation. With their help, then, a trench was dug through the mound's center "wide enough," Jefferson wrote, "for a man to walk through and examine its sides." This approach allowed Jefferson to inspect the mound for layers, or strata, a technique that would not enter the archaeological literature until Charles Lyell's Principles of Geology (1820). The various strata each contained bones covered by dirt, with the bones nearest the surface being the least decayed. Retrospectively, this has suggested that these remains were not as old, although Jefferson did not specifically draw that conclusion.

There are no field notes concerning the dig other than what is published in Notes. There is no evidence that Jefferson collected and kept any of the human remains for study. He made no mention of finding or collecting artifacts amid the human remains, an absence that conforms to the results of a 2003 study conducted by the University of Virginia at the very similar Rapidan Mound, in Orange County , Virginia. Jefferson likely conducted in-field analyses of the human remains and returned them to the trench.