"Every farmer in the region that's been affected has been impacted," Jo Shepperd from Queensland Farmers Federation said.
With supply routes cut, some dairy farmers were forced to dump milk, while growers are continuing to be impacted by transport delays and getting their produce to market she said.
Mango farmers who had already been struggling to produce a good crop in Queensland's north are now facing extensive damage.
One point two metres of rain fell over five days at Joe Morrow's mango farm near Mareeba where he's lost about half of his crop and half a million dollars of produce.
His 14 workers resumed harvest on Thursday after a two-week delay.
"Half my crop has either been damaged by the flooding, totally black, can't be harvested at all, or it's ripening and dropping onto the ground," he told AAP from his farm west of Cairns.
Mr Morrow is also the president of Queensland's fruit and vegetable growers association and said the damage to agriculture across the region has been severe.
"Every crop has been affected in some way," he said.
"Papaya trees are falling down, heavily blemished fruit, banana trees are falling down and sometimes some of that crop is also in water."
"Even the avocado crop which hasn't been harvested yet, there would be some impact on those growers as well."
Nursery owner Elaine Duncan is also counting the cost of the damage and will be continuing to clean up over the next week.
"The worst of it was the torrential rainfall and coming to work and seeing a nursery full of rotten plants."
It was probably around $300,000 to $500,000 worth of damage and loss of crop and ongoing trade," she said.
The nursery is a major grower of seedlings for far north Queensland, supplying home gardeners and hydroponic farmers with everything from tomatoes to basil and capsicums.
While the damage is still being assessed Queensland Farmers said it's likely to be several weeks before the full extent is known.
Disaster assistance loans of up to a quarter of a million dollars are available to producers impacted by the cyclone.