Graham Stanley Jones, 43, pleaded not guilty to one charge of dangerous driving at York Crown Court on Friday and was told he will go on trial later this year.
Jones, of Linton Woods Lane, Linton-on-Ouse, North Yorkshire, was charged after a single decker bus got stuck in flood water on a country road between the villages of Newton-on-Ouse and Tollerton, north of York.
The bus was transporting children to Easingwold School on January 5.
Jones stood in the dock for the 10-minute hearing wearing a grey suit with a white shirt and black tie.
Judge Paul Batty QC gave him unconditional bail.
Jones will go on trial at the same court on December 8. The trial is expected to last one day.