The process favoured applicants and submitters based in Auckland, with hearings held there while almost half of the submitters, many who wished to be heard, lived on Aotea, the appeal said.
Klink told the Herald there was "huge opposition" to the EPA decision on Aotea.
There were concerns the proposed activity would have an "irreversible impact on our moana".
"It is disgusting. It is going straight into wahi tapu (sacred places). Our tupuna spilt blood protecting those fishing grounds, and now they could be destroyed.
"People rely on the sea for food, and for work. There is no supermarket here."
Klink said the safest option was to place the dredged material on land.
They were planning a protest in Auckland at Aotea Square on July 6 ahead of the hearings to raise awareness about their plight.
The Society for the Protection of Aotea Community and Ecology raised similar points in its notice of appeal, adding the decision was also inconsistent with principles of the Treaty of Waitangi.
An EPA spokesman told the Herald they would not be making any comments during the High Court Appeals process.
In a statement in March, EPA general manager climate, land and oceans Siobhan Quayle said the application was publicly notified on July 30 last year, with a number of iwi authorities, customary marine titles, and protected customary rights groups directly notified.
There were 30 days for submissions to be lodged.
Ngāti Rehua-Ngātiwai ki Aotea Trust made a submission on the application, and representatives appeared at the hearing in Auckland to give evidence. Their information was provided and taken into account in the decision, Quayle said.
Staff had also visited Great Barrier Island and engaged with the Great Barrier Local Board on the application, Quayle said.
The EPA received 76 submissions about the application, with 83 per cent opposed, 12 per cent in favour, and 5 per cent supportive but with conditions.
Of those opposed, 38 per cent raised concerns about impacts on marine life, 21 per cent on water quality and 14 per cent on impacts on fishing.
The dump site covered about 7sq km and was about 25km east of Great Barrier Island and 22km north of Cuvier Island, a culturally significant site for founding tribes of the Te Arawa canoe.
The consent would replace CRL's current consent, which expires in 2032 and under which up to 50,000cu m of dredged material, from existing or proposed marinas in Auckland and Waikato, could be dumped annually.
Dredged material was first dumped at the site in 2010, in a test under Maritime New Zealand.
The initial application in 2009 was also challenged by iwi, who were concerned about potential impacts on marine life and the potential for marinas up and down the east coast to use the site.
Since then, between 100 and 130 barge loads had been dumped each year from dredgings at the Pine Harbour, Half Moon Bay, Sandspit, Hobsonville, Hobsonville Pt and Whitianga marinas.
In granting the application, the Decision Making Committee, appointed by the EPA, found any potential adverse environmental and commercial impacts would be restricted to the disposal area and be "negligible beyond the boundary".
Mitigation measures and conditions imposed on the consent would ensure "the biological diversity of marine species, ecosystems and processes in the Hauraki Gulf, and wider coastal and offshore environment, will be protected".
