The study, which is being carried out by Massey University and will include an up-to-date population estimate, is due to be completed next month.
DoC Bay of Islands manager Rolien Elliot said disturbance by vessels was one possible reason for the dolphins' decline, alongside food-source changes and environmental factors such as run-off.
It was too early to speculate on current dolphin numbers.
DoC was "generally happy" with the Bay's three licensed commercial dolphin-watching operators, and it was in their interest to ensure there were plenty of dolphins into the future. There were concerns, however, about some boaties.
"We were pretty disappointed in the behaviour of some recreational boaties last year, driving through the middle of pods. It's not good for the dolphins."
Local boaties were mostly familiar with the rules but some visitors claimed ignorance. As a result, DoC would step up its education efforts this summer and target Auckland's boating fraternity, for example through specialist magazines.
The dolphin rules include no more than three vessels with a pod at any one time, with other vessels to remain 300m away; no driving through pods; no-go areas such as Deep Water Cove, where dolphins are known to rest; a dolphin "lunch break" from 11.30am-1pm; and no swimming with dolphins if calves are present.
A moratorium on licences for new dolphin-watching operations, in place for the past three years, is due to expire in June 2016.
It may be lifted or extended, depending on the outcome of DoC's study. Tighter rules are another possibility.
Dr Constantine is trying to find out whether the Bay's missing dolphins have relocated to the Hauraki Gulf.
Two types of dolphin are frequently seen in Northland waters, common and bottlenose.
Bottlenose dolphins are nationally endangered and more often encountered in bays and harbours.
Common dolphins are smaller and have a "tricolour" pattern of dark grey on their backs, light grey flanks and cream bellies.
Bottlenose dolphins are larger and grey in colour with a lighter underside.
There are three populations of coastal bottlenose dolphins in New Zealand waters. The northeastern North Island population is found along the coast from the Bay of Plenty to Doubtless Bay.