Archaeologists, as well as police and a forensics team, were called to the College when bones and a crushed skull were unexpectedly unearthed by builders on Wednesday.
The remains of a second body were then uncovered on Thursday.
Some of the bones have been reported to contain bullet holes. A modern shell casing was also found on Tuesday, but is believed to be unconnected to the two bodies.
The discoveries were made by builders completing draining works outside Staircase Nine at the College.
Ken Macdonald, the Warden of the College, sent out an email to Wadham students saying: “You may know that skeletal human remains have been uncovered by the contractor excavating an area by the Elephant Gate to complete draining improvement works.
“The polices were called as standard procedure when human remains are unexpectedly found. As expected, archaeologists asked to attend the scene confirmed that the skeletal remains are archaeological.
“The skeleton remains of one adult human were uncovered yesterday and further remains of another human were uncovered today. The current view from the archaeologist is that the human remains are two burials, probably from the time when the site was part of the precinct of the medieval Austin Friary.”
He added: “I don’t need to labour the point that human remains should be treated with respect and dignity at all times. For this reason, entry to the contractor’s compound to view the remains is forbidden. I ask all members of College to respect this position.”
John Owen, a fourth-year History and German student, said: “What we’ve seen is a pile of bones and a crushed skull. It is rumoured to have bullet holes in it.
“Police have been here with a forensics team, and there will be archaeologists.”
Charlotte Lennon, a third-year Classical Archaeology and Ancient Historian, whose rooms is next to where the body was found, said: “As an archaeologist, I am very excited about the discovery of bones under my window.”
Thames Valley Police were unavailable for comment.