Federal MP Paul Neville says the floods have devastated southern Queensland's Wide Bay fishing industry.
He is appealing to the Federal Government to activate category D disaster relief funding, which allows exceptional circumstances grants to be made to primary producers.
Mr Neville, the Member for Hinkler, says fishers have been hit as hard as others in the sector.
"Twenty-one of the 28 trawlers operate through one facility here that's been damaged, so the trickle down effect of not getting category D here in itself will be horrendous," he said.
Burnett Heads fisherman Graham Stevenson says the commercial industry needs government assistance to get through the next few months.
Mr Stevenson says the amount of debris in the water has made it too dangerous for fishing boats to head out to sea.
He says some fish stocks have either been killed by the fresh water or are staying away from the muddy plume that has washed out of the Burnett River.
"There's other fishermen I know that their houses have gone under and some have lost boats and I don't know how they bounce back from that," he said.
"There's very little assistance while you own a fishing licence.
"It's very difficult to get assistance for a fisherman and that's the way it's been for decades."
He says the sector could do with some government help until conditions improve.
"Since the flood we had three years ago, every year the fishing was getting better," he said.
"When you've got a flood the juveniles survive better and so every year.
"If we don't get another massive whammy again every year should get better, but we're starting at zero and moving up."
Mr Stevenson says his catch could be almost non-existent for the next few months.
He says heavy flood debris and smashed-up boats have made it too dangerous to venture out to sea.
Mr Stevenson says the sharks and mackerel he usually catches would be staying away from the contaminated water that has been flowing from the river.
"A big plume has gone out from the river mouth, well out to sea, maybe 15 miles," he said.
"It's just muddy water that's carrying all the residue from whatever was in the city of Bundaberg ... whether it be oils and paints and pesticides - it's all mixed in, it's not a very good mix."
© ABC 2013
16:06 EST The weather bureau has implemented a new system of forecasting the seasonal outlook called Predictive Ocean Atmosphere Model for Australia, or POAMA.