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Port Chalmers Volunteer Fire Brigade Chief Fire Officer Stephen Hill said crews were called to Careys Bay about 5am.
They found fishing boat Echo submerged.
"Basically it was on the bottom," Mr Hill said.
It appeared the boat had a tide-related mishap, and got stuck between rising water and one of the piles on the pier, he said
The boat had docked on Monday evening with a full load of fish and planned to unload them yesterday morning.
Instead, emergency services used six pumps to attempt to refloat the vessel, assisted by winches on two other fishing boats.
Pumping went ahead throughout the morning, with the assistance of owner Gavin Heineman, who was in the water wearing a wetsuit.
The deck was under 1.5m of water and the hold had to be opened to get suction hoses in before being sealed so water could be pumped out.
"We managed to get enough water out of it to get it off the bottom, then we just kept going," Mr Hill said.
The vessel was refloated about 11am.
Mr Hill said it was a good outcome but Mr Heineman was "pretty devastated".
The salvage involved a big effort from crews from St Kilda and Ravensbourne fire stations, local fishermen and staff from the Otago Regional Council and D G Engineering, Mr Hill said.
Mr Heineman won a sustainability award in 2017 for designing and re-engineering the deck of Echo to include an aluminium chute for the crew to discard fish offal so seabirds would stay clear of the boat’s trawl cables.
Echo also made headlines when it saved a recreational fishing boat from sinking, by towing it to Carey’s Bay after responding to distress signals off the coast of Papanui Beach in September last year.