Prof Ewan Fordyce, of the University of Otago's department of geology, in waste deep water, used a concrete saw, chainsaw and finally a geology hammer to remove the footprint.
The footprint was then placed on a piece of plywood and covered to protect it from sunlight.
The footprints were found in early March by Ranfurly man Michael Johnston while he took his dogs for a swim.
Otago Museum marketing manager Hannah Molloy said earlier at 2.30pm the team was still trying to manage the water flow into the work site.
"There's a real balance between having enough water in to keep the pump going and enough out so the level drops.''
Once the prints were exposed they would start cleaning the prints and the work of cutting the fossils off would start.
"That's what we're all here for.''
The work was a much "slower and painstaking process'' than expected, she said.
"The timeframe will all depend on what they find when they start cutting them off, which they haven't done before.''
After the footprints were removed they would be secured onto another surface, wrapped and numbered so they could be transported to the museum.
There was a lot of activity at the isolated site today including a digger, large and small water pumps and a lot of media.
"The digger driver is amazing, he's so precise.''
The team would work until dark.
Once back at the museum the pieces would go into isolation spaces and its conservation manager would develop a plan of what to do with them and how to get them on display.
