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More than 30 chicks are nesting at Pilots Beach at present, and human intervention was needed because the chicks' parents were not returning daily to feed them.
Blue Penguins Pukekura scientist Hiltrun Ratz said there were about 500 adult Little Blue penguins in the area, and they were having problems finding food at the moment.
"Penguins are visual hunters. The food is there but they can't see it because the ocean is quite murky.
"We're finding that the penguins that live here and breed are only coming home sporadically - maybe only every three or four days.
"That's not enough. The chicks are losing condition and they can't grow properly."
Without supplementary feeding, the chicks would starve to death, she said.
It is believed the murky waters were caused by heavy rainfall and the resulting flooding of the Taieri and Clutha rivers in late November and early December.
Strong swells heading northeast over the past month had pushed the floodwater from the rivers back on to the coast around Dunedin, leaving large amounts of sediment in the water.
Dr Ratz said the chicks were being fed salmon smolt, and ranged in age from hatchlings to 12 weeks old.
Most chicks were able to fend for themselves once they reached 1200g - usually when they were eight weeks old - but some were staying until they were 12 weeks old because it was taking them longer to reach the 1200g weight range.
She said it was not the first time chicks in the area had required supplementary feeding.
"The project here started two and a-half years ago, but this is the first time we've encountered starving chicks in December.
"We've had starving chicks in February and March last year , but those were chicks that were abandoned by their parents because their parents wanted to moult.
"When they change their feathers, they can't go fishing because they're not waterproof.
"That's a time when they stay ashore for two and a-half weeks. If a parent is starting to moult, their chicks get abandoned."
She said the project was proving very successful and was helping to keep Little Blue penguin numbers up in the area.