Stewart and Janice Wagstaff have been accused of seven offences relating to "environmental permitting regulations" at the tip in Great Heck.
Mr Wagstaff, 54, and Mrs Wagstaff, 52, of Templar Close, Whitley, near Selby are due to appear at York Magistrates' Court on 17 February.
The tip was run by Wagstaff TWM until it went into liquidation in July 2015.
Two people have been charged over the operation of a North Yorkshire waste site, the Environment Agency has said.