Crayfish and snapper numbers are falling at the Goat Island Marine Reserve, north of Auckland, and scientists blame commercial fishing on the boundary.
The government is proposing to turn the inner Hauraki Gulf into a recreational fishing park, but those plans do not include crayfish.
Their numbers, and those of snapper, are now lower than before the Goat Island Reserve at Leigh was created in 1975.
Dr Nick Shears from the University of Auckland's Leigh Marine Laboratory said crayfish move out to the 800m reserve boundary to feed - and end up in commercial cray pots.
"Without replenishment into fisheries, and this is seen for the whole north-east of New Zealand, the crayfish fishery is going through a low patch at the moment.
"That's translating into low numbers inside the reserve as well so basically the fishermen, by fishing the boundary, are fishing down the numbers in the reserve."
Dr Shears said commercial fishing on the boundary started in the early 1990s, and it should be extended to 3km from shore so the crayfish have a chance to feed without being caught.
The Leigh Commercial Fishermen's Association supports the reserve, but would not comment on the effects of extending the boundary.
In a statement, it suggested increasing visitor numbers may be effecting biodiversity within the marine reserve and surrounding areas.
Last year more than 350,000 people visited the reserve.
The Sea Change - Tai Timu Tai Pari project has spent several years working on a Hauraki Gulf Marine Spatial Plan to protect the marine environment.
John Tregidga heads the Hauraki Gulf Forum, which is part of the Sea Change group, and said they did not want their plans overridden by the government's proposed recreational fishing park.
He was concerned that the government had not addressed different fisheries.
"We need to look at all the stresses that are happening, and one relates to the other, we do know that we want increased fish stock particularly around snapper.
"I'm also concerned about crayfish. Crayfish really have declined, and that's not in the recreational reserve which the minister is advocating for, which I'm a bit disappointed about."
Instead of complete no-fishing reserves Mr Tregidga would like to see fishing allowed when fish stocks are abundant.
But Dr Shears said that would prevent long term biodiversity gains.
As well as a drop in snapper and crayfish, reef fish stocks outside the reserve are also suffering, said Mr Shears.
"We're seeing higher abdundances in the reserve and that's due to a decline outside the reserve with this increasing pressure from new fishing techniques and a big increase in spear fishing.
"And just an increasing population, all these changes and increasing pressure on the environment is associated with the growing poplation in Auckland."
He said reserves will increase in value as more areas are over-fished, which means it's more important than ever to make sure they are designed properly and with the right boundaries.