The state's water use watchdog is investigating whether farmers have broken an embargo by illegally pumping water from the Namoi basin.
However, irrigators say the regulator sprung the embargo on water users last week, with the state government still yet to send out information about it to individual licence holders.
After the region got its first significant downpour in more than 18 months, the NSW government barred temporary water licence holders from drawing water from the catchment, despite rivers going above the legal threshold for the first time in months.
Namoi Water chief executive Jon-Maree Baker said while irrigators supported the embargo, there was a break down in communication.
"It's a bit like changing the speed limit on a road, not advising it, and then fining you for driving the normal speed limit," she said.
"I'd like to see a return to the previous process, where there was good stakeholder engagement and government advertisement about the situation and terms, and proper notification."
Many irrigators had already agreed to let the water pass by, even though they were entitled to take it before the embargo was put in place.
"We emailed out members on Sunday, advised them about the voluntary embargo - we felt that was the right thing to do for the health of the rivers and creeks," Ms Baker said.
The NSW Natural Resource Asset Regular (NRAR), said it had received reports regarding pumping in the Namoi last week.
"[We've] commenced an investigation into the legality of the pumping," NRAR chief regulatory officer Grant Barnes told the Leader.
"While it is possible the alleged water take is permitted under the embargo, the onus is on water users to be sure that they are operating within their licence conditions, and to check that there are no restrictions in place before they start pumping.
"NRAR staff have been on the ground this week in the Namoi and Macquarie, undertaking targeted and proactive monitoring of compliance.
"We will also be using remote sensing technology to support staff on the ground and increase our reach.
"These inspections will continue in the Namoi next week as the flows make their way through the system."