The Queen was greeted by children and well-wishers on her arrival at Hull's Paragon Interchange.
The Duke of Edinburgh enjoyed a walkabout among hundreds of people gathered in the city centre.
The Queen met members of Hull City FC, playing their first season in the Premier League, during her visit.
Several children presented the Queen with flowers.
Charleigh Kent, six, and her mother Charlene were among those who suffered in the flood of 2007 and who were invited to meet the Queen.