The harbour entrance is being deepened to accept the Royal Navy`s new aircraft carrier, HMS Queen Elizabeth, next spring.
The bomb is to be blown up in a controlled explosion after being towed out to sea.
Bomb disposal experts have chosen a spot about 1.5 miles (2.4km) east of the Isle of Wight.
"An unexploded German 500kg bomb has been found on the seabed in Portsmouth Harbour," a Royal Navy spokesman said.
"The device was located by a barge carrying out dredging works.
"A controlled explosion will be carried out between 10am and 11am by Royal Navy bomb disposal experts."
It is the second time World War II explosives have been found during the dredging operation.
A torpedo, discovered earlier this month, was exploded at sea.
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