About 30km of river channel is constrained by stopbanks in the scheme and spillways are constructed lower than stopbanks and designed to spill water into one of seven "pockets" of land. Each pocket has a pump station and water in pockets is pumped back into main river once levels have fallen. Farmers pay targeted rates of up to $71 a hectare to pay for running the scheme.
The farmers contend in their statement of claim that they made submissions on the consent application when it was lodged in 2004, but the WDC applied to amend the consent application in 2009 to include altering the length of certain spillways and stop banks.
The farmers say a review of the amended application by the NRC did not assess whether the amended application should be publicly notified.
Spokesman for the group and fellow swamp farmer Ben Smith says the farmers contend the alterations made directly affect them and their livelihoods and that they should have been notified and allowed to make submissions on the amended application.
"By not being allowed to make submissions we have had our democratic rights trampled on," he said.
Mr Smith said the changes to the spillways and stop banks directly and adversely affected the farmers.
"For us, the last big flood cost more than $95,000 in regrassing and feed. We've got to the end of our tether with the councils and feel we have no option but to take this court action," he said.
The farmers seek to have the court rule the granting of the amended consent was invalid and to quash the decision. They also want the amended application to be now publicly notified and seek costs from the two councils.
A Whangarei District Council spokesman said the authority would not comment as the matter was now before the court.
The scheme has been operating since the early 1950s and the WDC were given responsibility for it after the 1989 local government reforms.