Farmers that rely on Queensland's Flinders River say some regions are missing out on their fair share of water.

The Queensland Government last week opened a new tender process to divide up 250,000 megalitres (ML) of water between five catchments areas.

The bulk of it will go to producers on the banks of the Flinders and Cloncurry Rivers, leaving just 25,000 ML for landholders between Torrens Creek and Richmond.

Mr Lynham claims the water allocations were split up so that small producers would get a chance to make a successful bid.

“Previously everyone would have had to tender for the bulk amount of water, and you would have seen some of the larger producers taking more and the small producers competing against them,” he said.

“Now, because it's staged through the catchment system, everyone in a specific region can apply for a specific amount of water.

“Up in the headwater we've released over 60,000 ML of water where farmers, who tend to be smaller, can have that.

“Further down the catchment, the larger producers tend to be there.”

But irrigators in the Flinders River Ag Precinct say the larger allocations for producers in the Gulf of Carpentaria are “tied up” in pastoral company Stanbroke's Three Rivers Project.

The company wants 120,000 ML of water to grow 15,000 hectares of cotton on Glenore cattle station, near Normanton, and successfully secured a water allocation in the last round of tenders.

Flinders River Ag Precinct chair Brendan McNamara has told the ABC that it is disappointing a majority of the water has been allocated further north.

“The thing that we were looking for was for the water to be spread out pretty evenly around the river, to get some good economic development going in the different areas,” he said.