Granite Island's small and fragile colony of little penguins has recorded a "significant increase" in numbers despite South Australia's ongoing harmful algal bloom.

A team of 56 volunteers scoured the island looking for active and inactive burrows, as researchers calculated the number of adult birds returning to the island each night.

Diane Colombelli-Negrel, from Flinders University, said the census found 18 active burrows, suggesting an adult population of 36 birds.

"It's a significant increase. We had 30 birds last year so … it's promising,"

Dr Colombelli-Negrel said.

She said "so far" it appeared the state's ongoing algal bloom was not affecting the Granite Island penguins.

"It doesn't mean it can't affect them in the future, but at the moment we are seeing increasing numbers and

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