A report showing an "alarming" rate of decline in fragile marine environments in the Marlborough Sounds has confirmed long-held concerns of scientists and the local authority.
Damage is being caused by dredging, boats anchoring and the effects of flooding and post-harvest forestry run-off into the sea.
Marine biologist Rob Davidson, who authored the report, said today the damage threatened large numbers of interconnected marine species, of which few were now left.
"It was quite a shock really. We know that we have lost a lot of areas, and the signficant areas we have left are remnants of, probably, what was much more widespread."
He said a driving force behind the report was to identify and rank the "important bits" of the area that were left - based on factors such as the presence of iconic species, the presence of endangered species, and whether a habitat was the best example of its kind.
The research found 1300 hectares of marine habitat was destroyed between 2011 and 2015, more than 71 percent of the area originally surveyed.
Marlborough District Council said it would now work more closely with industries linked to activities harming marine areas.
Environment committee chairman Peter Jerram said the council was stunned at the speed of change in the areas surveyed, and the report had highlighted long-held concerns.
"In a way [the marine areas] are a bit like ancient pieces of native bush but because they're below the sea, and no one sees them we weren't aware of them.
"But the council does have a statutory responsibility to preserve biodiversity but also to monitor the state of the environment."
Mr Jerram said he was not hopeful that planned new forestry standards in their current form would help the situation.
The report, which takes in analysis over a four-year period, was jointly funded by the council and the Department of Conservation.