"In contrast, there was no effect of marine reserves on snapper under the legal size limit."
Possible reasons for the varying effects of the three reserves include differences in reserve size, habitat, and how well the reserve was enforced, he said.
Large, well-enforced reserves in good habitats were crucial to their success.
Snappers were generally shy of scuba divers and estimating their numbers was a difficult task.
"As a wise colleague once said, 'Counting fish is like counting trees, except you can't see them and they move'," Mr Smith said.
The study authors chose to use a "baited underwater video", where a video camera is aimed at a box of bait for a fixed length of time.
The maximum number of fish seen in one frame is then used to ensure the same fish is never counted twice. Data from fish counts is notoriously difficult to analyse and often hugely variable, but the Massey scientists developed novel statistical methods that allowed them to produce the most accurate estimates of New Zealand marine reserve effects to date.
This research is timely, as marine spatial planning of the Hauraki Gulf is under way and new marine reserves are likely to play a key role.
Watch: Tuhua Marine Reserve monitoring
As well as being a proven drawcard for ecotourism, marine reserves also had a wide range of potential ecological benefits, the paper said.
Snapper were important predators of kina, which could reduce kelp forests to bare rock if their populations were unchecked, while large numbers of hefty fish in marine reserves could also act as "reproductive reservoirs".
The paper comes as government changes to snapper fishing in an area that takes in the gulf come into effect today.
The total allowable catch in the area has been increased from 7550 tonnes a year to 8050, the extra 500 tonnes being allocated to the recreational sector.
But the changes also include a cut in the bag limit from nine to seven a day and an increase in the minimum size from 27cm to 30cm.
Online survey to help map future of the gulf
An online survey that will help officials to develop a spatial plan for the Hauraki Gulf is asking people what they do in the region's marine playground.
The survey, developed by AUT University PhD student Rebecca Jarvis and running until April 21, will ultimately provide extra information for the two-year SeaChange project.
Ms Jarvis said it was anonymous and the resulting map of what people do, where and why, would be shared with the public.
"By providing the opportunity for people to have their say, the survey will provide geo-spatial data on how they use and value the gulf, integrating different social and cultural considerations into spatial planning," she said.
"We hope to gather the views of as many people as possible, including those who live outside the region."
Take the survey here: www.seachange.org.nz/survey
Fish in the sea
*Massey University scientists used underwater cameras and specially developed statistical methods to count snapper at marine reserves in the wider Hauraki Gulf region.
*The biggest difference between snapper numbers - 20 times greater than that in fished areas - was observed at New Zealand's oldest reserve, the popular Cape Rodney-Okakari Pt (Goat Island) Marine Reserve near Leigh.
*The estimated effects of the other reserves studied were eight times at Tawharanui and 16 times at Whanganui a Hei (Cathedral Cove).
*The average effect size across reserves was 13 times.
