The boat, formerly known as Paid For, was undergoing renovations and relied on a bilge pump to stay above the Savannah River.
At some point Monday evening, a power cord plugged into the marina's power source was stolen and the pumping stopped.
By 7 a.m., only the top of the pilot house was above water.
"The owner did a good job keeping it up so there was no oil in the water," said Tonya Bonitatibus, the executive director of the Savannah Riverkeeper.
A dive team hired by the boat's owner bailed out the vessel throughout the day and buoyed it with inflatable tubes.
Around 4:30 p.m. Tuesday, the boat had mostly re-emerged from the chilly Savannah, but there was still considerable work left to do.
A man identified as the owner declined to comment.
Witnesses said the 20-year-old boat, with faded gray paint, formerly belonged to North Augusta High School's Navy Junior ROTC.
Randy Scott has a boat docked alongside the sunken vessel and said thieves have been stealing power cords for a week.
He lost power to his refrigerator and other appliances when thieves stole his cords, which cost more than $80 apiece. Later, thieves stole electronics from his boat.
The east end of the marina, which borders Riverwalk Augusta, doesn't have a tall security fence like the other two portions.
"That's the million-dollar question," said Barry Goff, who has docked at the city marina for nine years.
Mike Stacy, who leases the marina from the city, said Tuesday that is just the way the marina was built.
He said that in the near future he plans to ask Augusta's Ports Authority to construct a security fence to keep out trespassers.
Until then, Stacy is offering a $500 reward for anyone with information that leads to an arrest in the thefts.