The SpecialAreas of Conservation at the Maidens include sandbanks, reefs and grey seals, while the areas protected at the Skerries and Causeway includes sea caves, sandbanks and reefs.
"The risk of likely significant effects on the integrity of the specialareas of conservation cannot be excluded on the basis of objective information, " he said.
The SpecialAreas of Conservation include the sea and seabed surrounding the Maidens Islands off Larne and those adjacent to the Portrush Skerries and Giant's Causeway.
Mr Justice Stephens found that there had been a failure to carry out an appropriate assessment of the rivers Foyle and Finn specialareas of conservation under the Habitats Directive.
The judge had previously said he was minded to quash the decision to proceed with the project because, he said, the department had failed to carry out an appropriate assessment of the rivers Foyle and Finn specialareas of conservation under the Habitats Directive.
The River Hart flows through the rural area which has 1, 000 buildings listed as being of special architectural or historical interest and more than 30 conservationareas.