The Sierra Club and the Audubon Society asked the the Environmental Appeals Board and Coastal Zone Act Industrial Control Board to rule on appeal.
Superior Court Judge Andrea L. Rocanelli ruled neither group had the jurisdiction to hear the appeal.
The two environmental groups have claimed the loading of oil violated the state’s Coastal Zone Act and have spoken in opposition to the environmental permitting for the refinery.
Opponents have also claimed that construction of a rail yard that receives crude oil from North Dakota and Canada for use at the refinery violates the Coastal Zone Act, which bars new heavy industry in that area.
The rail yard and other changes have been credited with helping the refinery remaining profitable.
Former owner Valero shuttered the refinery during the economic downturn and was moving toward demolishing the facility before PBF Energy agreed to buy the site with assistance from the State of Delaware.
The refinery employs about 500, with hundreds of additional workers at the site at various times.