An elderly cyclist drowned when he was swept away by flood waters in the town of Castel Bolognese, Ansa news agency reported.
The body of a man aged around 70 was found in an house that collapsed in the nearby village of Fontanelice, a spokesman for the fire service told Reuters.
The rain follows months of drought which raised concerns about the low water level in the Po, Italy's largest river, which runs West to East through the northern part of Emilia Romagna.
Prime Minister Giorgia Meloni said in a statement she was in "constant contact" with the authorities involved and expressed "solidarity and closeness" to those affected by the flooding.
Footage released by the fire brigade showed extensive flooding in an area between Bologna, Emilia Romagna's capital, and the city of Ravenna on the Adriatic coast.
The fire brigade said it had carried out around 400 rescue operations, evacuating dozens of people.
Rail operator Trenitalia said several services were suspended while a number of streets were closed.
The head of Italy's civil protection agency said he was travelling to the flood-hit area and Environment Minister Gilberto Pichetto Fratin promised help for those affected.
"The government stands by the people in difficulty: today for the emergency, which must be backed by adequate economic resources, but from now on to accelerate (infrastructure) measures that are needed for safety," he wrote on Facebook.
(Reporting by Angelo Amante, editing by Gavin Jones, Bernadette Baum and Nick Macfie)
