The new evidence disputes the notion that the Hunley was damaged and took on water after ramming a spar with a charge of black powder into the Union blockade ship Housatonic.
Scientists studying the sub said they've found its pump system was not set to remove water from the crew compartment as might be expected if it were being flooded.
The sub, located in 1995 and raised five years later, had a complex pumping system that could be switched to remove water or operate ballast tanks used to submerge and surface.
"It now really starts to point to a lack of oxygen making them unconscious," said state Sen. Glenn McConnell, R-Charleston and the chairman of the South Carolina Hunley Commission, formed to raise, conserve and display the sub. "They may have been cranking and moving and it was a miscalculation as to how much oxygen they had."
In excavating the sub, scientists found little intermingling of the crew remains, indicating members died at their stations. Those bones likely would have been jumbled if the crew tried to make it to the hatches in a desperate attempt to get out.
"Whatever occurred, occurred quickly and unexpectedly," McConnell said. "It appears they were either unconscious because of the concussion (from the attack) or they were unconscious because of a lack of oxygen."
Archaeologist Maria Jacobsen cautioned that scientists have not yet examined all the valves to see if the crew may have been trying to surface by using the pumps to jettison ballast.
"Can we definitely say they weren't pumping like mad to get water out of the tanks? No we cannot," she said. "I'm not really at a point where I think we should really be talking about what these guys were doing at the very end because we simply don't know all the valve settings."
But she said scientists can definitely say the valve that would have been used to remove water from the crew compartment was closed.