The Hastings river oyster industry is looking at at least $500,000 in damage after the worst flood in more than 30 years.
Infrastructure like pontoons and oyster racks have been ripped out by the surging river.
Local grower Mark Bulley said the industry was not prepared for the speed the floodwaters hit, and the local damage could impact on the industry statewide.
"We've got to hope for the best in this scenario that we don't get too much of a loss and the impacts could be felt across the industry," he said.
"The Hastings River supplies about 20 percent of the juvenile stock to the rest of the NSW industry so it could be a bit of a flow on effect from here."
Mr Bulley said farmers tried to prepare for the event, but were caught-out by its speed and ferocity.
He says infrastructure worth over half a million dollars has been lost but damage to shellfish will take longer to assess.
"We've got to wait for the estuary comes back to full saline conditions and then depends how well the oysters recover from the fresh,' he said.
"It's not so much the fresh water that's a concern, it's what could be in the fresh water.
"There's whole modules of oysters that have gone, whole rafts that have just disappeared.
'We've managed to get most of the drums and that back but you know guys have got 25ml ropes on these and they're running four ropes and they've just broken.
"It was like snapping dental floss."
© ABC 2013
13:56 EDT Like a large area of southeastern Australia, Victoria has been been experiencing a chilly run, as much as four-to-ten degrees below average but is now thawing out.