The boat, moored at Snug Cove, was last seen afloat at 12.30am on Tuesday morning but owner Michael Standen received a 5.30am phone call from an Eden tugboat driver.

"They told me my boat was on the bottom," Mr Standen said.

"Ultimately it was the weather that caused the sinking, the wind had tossed so much water into the boat.

"The pumps run off the electricity supply but it is only a finite supply.

"They just ran out," he said.

On Wednesday at 10am Mr Standen and Reuban Shaw dived to inspect the boat before attaching ropes and chains to the vessel.

Nik Cetkovic of Nik's Crane drew the sodden boat to the wharf and raised it enough for pumps to drain about three tonne of water from the holds and deck.

Initially attached to the bow, the ropes had to be moved to the stern when 3.5 tonne of lifting power couldn't budge the boat.

Dizzy from the boats fuel fumes which had seeped into their regulators, both divers were pleased to be out of the cold water at 3pm.

"From what I could see the boat's a write off," said Mr Shaw.

Eden harbour master Jo Clark said that there was no environmental damage from the capsize.

"We were watching it pretty closely," she said.

"Because it's unleaded petrol it more or less evaporates.

"There was also a few litres of sump oil on board but it's all been well contained.

"It's been quite a simple one from our point of view," Mrs Clark said.

Snug Cove's breakwater wharf provides protection from south-easterly winds, however leaves the harbour and many boats vulnerable to weather caused by south and south-westerly winds.

"Weather from the south and south-west is always bad in that harbour," Mr Standen said.

"The waves are picked up all across Twofold Bay and into the throat of the harbour.

"Even when we got down there at about 6am the wind was still ferocious," he said.

At the time of going to press pumps were emptying the boat of seawater in order to lift it onto its trailer for removal to Merimbula.