Traditionally, the Ministry for Primary Industries and Department of Conservation have been responsible for rules around how plants and animals are managed in the marine environment.
The Environment Court ruling means that regional councils now have a role to play in protecting marine biodiversity around these three reefs.
The minister's sign off is the next step in this unique process, which now leads to regional council needing to determine an implementation date.
Regional council's regulatory services general manager Sarah Omundsen said the community could expect to see the rules in place for next summer.
"There will be a focus on education and information-sharing leading up to the new rules taking effect. We'll be ensuring a fair and reasonable notice period so everyone can get prepared and do their bit to protect this area's marine biodiversity."
Omundsen said planning for a public education campaign was well underway and details of the protected areas and how people could help look after these reefs, would be in local newspapers, community newsletters, on boat ramp signage, on the regional council's website and social media.
"Over the coming weeks we will be working through the next steps, including determining a date the rules will apply. We know that this has come about through an unusual process, and will be working with tangata whenua and a number of groups in the community, including recreational and commercial fishing groups.
"We are also collaborating with other government agencies, including the Ministry for Primary Industries and Department of Conservation, for the best outcomes.
"We can all agree that the marine environment is worth protecting for future generations and by following the new rules, everyone can do their bit to protect these reefs and their ecosystems too."
Bay of Plenty Regional Council deputy chair and chair of the coastal plan sub-committee, Jane Nees said it was excellent to finally have the regional coastal plan appeals resolved, providing direction and certainty for the community.
She said it had been a long process for everyone involved but was now another step in the right direction to preserve our coastal treasures.
"This is a unique and complex case, resulting from a decision by the Environment Court. As a result, there has not been specific public consultation, as the proposed protection areas were not included as part of the proposed Regional Coastal Environment Plan that was consulted on in 2015.
"However, we are committed to providing clarity around what the Motiti Protection Area means for our community, why the Regional Council is involved, and will be working with tāngata whenua and all stakeholders to make sure the new rules are well understood with plenty of notice before they come into effect this year," Nees said.
The regional council has started environmental monitoring within the Motiti Protection Areas to establish a baseline for how the reef ecology looks today, before the reefs are protected.
This data will then be used for years to come as a reference point to determine if the protections put in place by the court are achieving the desired biodiversity outcomes.
The Regional Coastal Environment Plan promotes the sustainable management of the natural and physical resources of the Bay of Plenty's coastal environment.
