The indictment was issued late last week against Lance Charen, a former manager for International Petroleum Corp.
Charen is charged with improperly handling hazardous waste, falsifying reports, tampering with monitoring devices, and other crimes.
Defense attorney Kerry Kalmbach said Charen will plead not guilty at a March court appearance.
Authorities say IPC, which operated the facility from 1992 to 2012, routinely falsified reports about the amount of chemicals being dumped into Wilmington's sewer system.
IPC pleaded guilty earlier this month to conspiring to violate the Clean Water Act and transporting hazardous waste without a manifest. It was ordered to pay a $1.3 million fine and $2.2 million in restitution to the city.