The man, believed to be a 73-year-old from Oxford, died at the John Radcliffe Hospital after getting into difficulty on Godstow Road, Wytham.
Thames Valley Police said the man's next of kin had been informed but no formal identification has been made.
The Environment Agency said several flood warnings were in place in Oxfordshire, with dozens of homes flooded.
Oxfordshire Police's Supt Christian Bunt said the force's "thoughts are with the family of the man who has died".
"This appears to be the second tragic incident in which someone has died after entering floodwater in the Oxford area in the past few days.
"I wish to reiterate my warning that the public should take extra care to ensure they do not put their lives at risk by entering floodwater."
On Saturday, a 47-year-old man on a mobility scooter was killed while trying to pass a flooded pathway.