The kelp forests are mostly invisible from the shore except when storms wash strands onto Lady Bay's beach along with a spongy blanket of other seaweeds.

But this year the iconic giant kelp species that can tower up to 12 metres off Warrnambool has appeared "patchy" to scientists using drones and sonar mapping.

Deakin University Warrnambool's Dr Daniel Ierodiaconou said a lack of long-term data meant it was unknown how much kelp was lost, but he and a team of researchers have now laid the groundwork to monitor the changing forests.

"There seems to be a lack of dense giant kelp beds out there this year," he said.

"They may not persist as they used to and the consequences of such a loss is concerning."

The underwater forests are a habitat for the region's rock lobster and abalone and researchers say kelp forests are known to absorb 20-times more carbon dioxide than some forests on land.

The federal government listed giant kelp in south-east Australia as endangered in 2012 due to changing ocean conditions caused by climate change.

As the East Australian Current pushes warmer waters down Australia's eastern coast, kelp forests off New South Wales and Tasmania have seen dramatic losses and Victorian forests are not immune, Dr Ierodiaconou says.

The kelp forests may also work in Warrnambool's Lady Bay as a buffer against erosion.

"If you think about this three-dimensional structure in the water, and the waves that come from the Southern Ocean and hit our coast, those kelps are actually absorbing a lot of that energy, acting as a nature based coastal defense," Dr Ierodiaconou said.

"Once these kelps and other seaweed end up on the beach as wrack they can form a natural defense to coastal erosion by helping to trap sediment and absorb wave energy."

"What we are finding is we are losing these structural habitats and that's changing the ecology."

He said giant kelp are seen across south-west Victoria from the Hopkins River west to the Glenelg Estuary and form an important part of the Great Southern Reef that extends across Southern Australia.

A map from 1870 that marks small trees in ocean off Warrnambool is the first written record of kelp forests in Lady Bay.

"The traditional owners would have had a much longer association with these seaweeds and the diverse communities they support that would have provided important food sources," Dr Ierodiaconou said.

Scientists have now collected 15 years of records of the changing seabed off Warrnambool, including mapping kelp using sonar systems, underwater camera systems, diver surveys and drone footage.

"We have done quite a bit of monitoring in the past but it's really through building these long time-series that you really get an understanding of what's happening," Dr Ierodiaconou said.

"The technology we have available provides a picture that has been incomprehensible in the past."

Meanwhile, Dr Ierodiaconou said his team assisted in deploying an oceanographic mooring in the Bonney Coast Upwelling off Portland and have also played a major role in setting up a wave buoy network across Victoria for the first time.

He said the Bonney Upwelling mooring was measuring a strong seasonal upwelling of cold nutrient rich water that supports one of the most productive regions of Australian coastal waters.

"The mooring is measuring temperatures through the water column, currents and ocean acidification" Dr Ierodiaconou said.

"The upwelling system is likely to amplify the impacts of ocean acidification as the cool deep water upwelled is likely to be more acidic. This will likely have impacts to the entire foodweb, especially those critters with fragile shells.

"We believe that the mooring is going to be like the canary in the coalmine measuring the impact of climate change in our oceans."

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