Mr Cowper said a decision by the Office of Water six weeks ago to stop releasing water from the dam into the river was not only impacting on landowners and the environment but also contravening a government agreement.
"An agreement signed when the dam was opened in 1994 provided for regular releases of water from the dam to sustain the river environment and also to adequately provide for the riparian water rights of a dozen or so downstream farmers," he said.
"The agreement provided for releases to stop at the beginning of winter after opening falls of 60mm or more of rainfall, but an on-site ranger liaised with landowners to ensure their needs were met.
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READ NOW"All of this clicked in after 61mm of rain was recorded back in April, but water management procedures at North Dandalup Dam have changed. The on-site ranger can no longer sanction water releases when they are necessary, and there has been no rain since."
Mr Cowper said refusals by the water administration to restore environmental flows to the river in the absence of more rain had led to needless stress for landowners and the environment.
"At around the halfway mark, the North Dandalup dam is at its highest level since construction.
"It has been receiving winter top-ups from both the Stirling Dam at Harvey and from the Binningup desalination plant to ensure adequate drinking water for Perth.
"There is therefore no valid reason for the river system in front of the dam wall to be denied adequate water.
"Here is an opportunity for the minister to bring her bureaucrats into line to ensure that an important, long-standing agreement is honoured between landowners and the local community."
A spokesman said the Department of Water would meet with North Dandalup downstream landholders next month to discuss the drying climate, the current release regime and the communication protocol around it.
Some downstream users had made the responsible decision to start moving to alternative sources such as groundwater or rainwater tanks, given the predicted long-term drying trend.
There had been significant consultation with downstream users of North Dandalup Dam to address concerns about low-flow and cease-to-flow conditions.
The water release regime and management for North Dandalup had been generally consistent this year with previous years.