"It gives (the harbour) a break, and lets it do what it needs to do, and that's regenerate," she said.
"We can't have dredging in there. It's a different environment down there to what it was 20 years ago."
Porter-Manuel said the marae was working in collaboration with the Ministry for Primary Industries, and had had a lot of community support for the rāhui.
Rāhui adviser Reuben Taipari said the two 100-year floods that hit Kāeo in 2007 had done a lot of damage.
"When Kāeo flooded, sediment washed into the harbour and covered the scallop beds, and they haven't been able to recover because people are still harvesting them," he said.
"A rāhui is needed so they can recover and establish themselves again, and so we can harvest properly.
"Everything else is fine - kina, snapper, oysters - it's nothing to do with the marine environment, it's to do with the seabed that needs to be left alone. If nothing's done, scallops will become extinct in the Whangaroa Harbour."
Taipari said the area would be monitored by local hapū, who would undergo training. Signs explaining the rāhui would be erected at various locations, including at boat ramps. Seasonal and annual reports would be given to the marae and MPI.
"Hopefully in two to three years we'll be back on track," Taipari said.
Former NIWA marine biologist Ken Grange, who lives in Kerikeri and was at the hui to share his knowledge, said recovery was possible.
"If the habitat is still there and hasn't been too damaged by dredging there's a possibility they'll come back," he said.
"They need lots of them in an area to successfully breed, however. If you don't have enough adults together the sperm and eggs don't mix and fertilise. They need to be left alone to make sure their habitat is okay so it can self-generate, then it should be able to look after itself.
"What the rāhui may also do is allow a bit of research on growth rates or survival."
Whangaroa resident Ross Guy, president of Kāeo Hunting and Fishing Club, said he supported the rāhui as long as it was consistent and applied to everyone.
"It's got to be good," he said.
"Twenty years ago there were heaps of scallops, and two or three years ago we couldn't find any.
"They move around a lot and there's probably too much silt going into the harbour, and too many fellas from out of town. If you have a look at the fishing along there everyone's on a 6-7m trailer boat."