Niwa marine ecologist Leigh Tait said the Niwa drone team was working with the Department of Conservation and University of Canterbury to map marine reserves at Okarito (near Franz Josef) and Punakaiki.
Dr Tait said parts of the West Coast were so dangerous for humans to access marine biologists had no idea what plants and animals were there, or how they were faring.
The drones had opened up a whole new method of gaining valuable insight into the marine environments.
"One of my major concerns is that traditional monitoring methods, such as transects and quadrats [sampling at specific points], only cover small areas and are selected mainly because they’re accessible.
"We’ve missed a whole lot of habitats just because we can’t physically sample them."
Of particular interest were the large kelp beds just off the coast, which were "sentinels" of the habitats they protected.
"They’re the species that really drives productivity and offers the kind of habitat a lot of fish and animals need to survive.
"A lot of things hide in the kelp, a lot eat it and a lot of animals rely on it indirectly. They are the signs of a healthy ecosystem."
The drone imagery is captured using multi-spectral cameras — essentially six different cameras, each recording a different portion of the light spectrum.
Dr Tait said data collected by the drones would enable him to map those beds, discover how extensive they were and provide an estimate of the coverage of other key habitat types.
Baseline maps would be produced to enable consistent long-term monitoring.
The information was being collected ahead of an expected marine heatwave this summer, which would enable comparisons to be made about the effect of warmer sea surface temperatures on the kelp beds, he said.
