Conservationists say they are breathing a sigh of relief as environmental water flows reach the Macquarie Marshes after the federal government lifted pauses on environmental releases.

The Commonwealth Environmental Water Holder (CEWH) placed the pause in mid-August following a new interpretation of water metering rules.

CEWH leader Dr Simon Banks said on 12 September that they are now compliant with the rules for most watering actions.

However, it's unclear whether the resumption of releases was due to a reinterpretation, recent changes to water rules or a legal work-around.

"The decision to lift the pause in some circumstances follows careful consideration and analysis of the regulatory requirements of each Commonwealth environmental watering action," Dr Banks said.

"This included engagement with the NSW Department of Climate Change, Energy the Environment and Water (DCCEEW).

The Macquarie Marshes is an internationally recognised wetland attached to the Macquarie River. [IMAGE: River McCrossen]

"It is likely that some Commonwealth watering actions will need to remain paused for some time, while NSW works to ensure metering compliance or alternative measurement methods are assured for remaining actions."

The pause came within weeks of a planned release from Burrendong Dam into the Macquarie River, which triggered concern that the system would not receive the water needed for conservation efforts.

Narromine-based Tony Lees has been involved in native fish repopulation within the river, which relies on flows from the dam released within a certain window. 

The release went ahead after the unpause and Mr Lees said they made the window, although he also said it could have been more effective "a week or two ago."

"In the scheme of things, we think that we'll get the result we're trying to get," Mr Lees said.

"It was such turmoil knowing that we would be set back for years trying to protect the Marshes if we missed one year.

"The BOM (Bureau of Meteorology) is telling us that we're looking at about 70 to 80 per cent chance of better rainfall in this coming season, so everything's sort of pointing towards a successful breeding season."

This month, the NSW Parliament also passed changes to water rules which Dr Banks said will allow more watering work to resume.

Commonwealth Environmental Water Holder Dr Simon Banks. [IMAGE: CEWH]

The pauses centred around what authorities should consider 'take,' which refers to water removed from a stream for use outside the system.

The Water Holder has not clarified what the previous interpretation was, although water used to improve river health can now be considered 'take'.

That would mean it has to be pumped and metered, which critics say creates unnecessary infrastructure costs and defeats the point of leaving environmental water in the river.

Water action in the Barwon-Darling River is also planned in the coming weeks, according to the (CEWH), which will be measured at a Bourke weir.

However, the Nature Conversation Council's Mel Gray said that the amendments are a "band-aid solution."

"We've got a law that's old and teetering on amendment after amendment," she said.

"We obviously need a minister to look at rewriting, or at least reviewing, the Water Management Act."

Researcher at water consultancy Slattery and Johnson, Maryanne Slattery, said the amendments provide clarity for environmental water licensees, although she said a regulatory solution could have been unnecessary.

However, she said it's difficult to know since governments have not explained the problems in detail or publicised their legal advice.

"When I first heard about the stop on environmental watering, I thought the legal request must have been very narrow and probably naive. 

"Seeing the regulation, I stand by that original assessment, because there's things in that are incorrect and unnecessary," she said.

"However, the amending regulation might be necessary for the environmental water holders to believe they've got the legal cover to undertake environmental watering."