An examination revealed the skull had been penetrated by what could have been an iron arrow or spear.
This identified them as medieval, from between AD1066 and 1540, but they could even be Roman or Saxon, experts said.
The remains came from the River Lark at West Row near Mildenhall and the police were called in the first instance.
Nearby battle
Ryan Ely, from the Environment Agency, said: "We had not expected to find any remains but had taken advice from Suffolk's archaeological service before we started dredging.
"Dragline operator, Simon Wenn, was on the alert and, after his grim discovery, we turned to the archaeological service once the police had given us the all-clear."
More bones, including those from a juvenile and a 14th century metal buckle were also recovered during the work.
The circumstances of the adult's death are unknown although there was a battle at Fornham in 1173, but this association is pure speculation.
There have been other finds from Suffolk rivers in the past but this is the first find from this area for several years.
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