More than 10 years on from the high court decision on Blue Mud Bay – which gave Aboriginal traditional owners control over who fishes in their coastal waters, and sparked a bitter battle with fishers and the Northern Territory government – settlement has finally been reached.

In 2008, the high court said that traditional owners of Blue Mud Bay had exclusive access rights to waters which sit on Aboriginal land – like the intertidal zones of oceans and rivers – affecting up to 80% of the NT coastline.

The decision alarmed amateur and commercial fishers, and tourist operators in the Top End, but represented a chance for traditional owners to reap the economic, cultural and environmental benefits of control over their own waters and fisheries management.

Wednesday’s deal, signed at Nitmiluk (Katherine Gorge), is between the first nations people who have rights, interests and responsibilities along more than 6,000 kilometres of coastline, the NT government, the Amateur Fishermen’s Association of the NT, the NT Seafood Council and the NT Guided Fishing Industry Association.

The Northern Land Council chief executive, Marion Scrymgour, is “delighted that this matter is finally being resolved. The settlement arrangements are exciting and offer great opportunities. I believe this package will genuinely assist reconciliation.”

The Blue Mud Bay agreement signed at Nitmiluk, near Katherine, by fishing groups, the Northern Land Council and the NT chief minister, Michael Gunner.

Under the agreement, amateur fishers will not need permits for the greater Darwin region, including the area from the Daly River to the East Alligator river, where most recreational fishing occurs.

But those arrangements will be reviewed as outstanding land claims are settled in the region.

Other areas, such as the Roper River, may be open to long-term access agreements in the future.

Codes of conduct will be developed for fishers, and traditional owners will become actively involved in the commercial fishing industry.

There will also be a comprehensive review of NT fisheries management, legislation and policy, according to the agreement giving Aboriginal people real input to management of their waters.

“Settling Blue Mud Bay has been a complex process,” the Northern Land Council deputy chairman, John Christophersen, said. “Finally we can all move forward together, developing world’s best fisheries management approaches for the NT, and where management is driven by good science rather than politics for the benefit of all Territorians.”

The president of the Amateur Fishermen’s Association, Warren de With, said: “Today is the culmination of years of hard work and cooperation. It paves the way for certainty and for a bright future for recreational fishing in the territory.”