Murray Darling Basin Authority reports on river health have found declining native fish populations, ongoing water-quality issues and insufficient flood-plain watering despite the recovery of 2135 gigalitres of annual water entitlements to the system over 13 years.
Balancing the needs of basin's environment with its 2.4 million residents, more than 50 Indigenous nations and the communities, farms and businesses that depended on it was no easy task, authority chief executive Andrew McConville said.
"It's clear from the results that the Basin Plan is working, but there is more to be done," he said.
"What we do next will determine the long-term health of the basin."
Full implementation of the plan and its ultimate goal of returning 3200 gigalitres to the environment was a long and costly way off, with the most cost-effective approaches to water efficiency already exhausted, the report found.
Hydrology reports found the basin had become hotter and drier in recent years, as increased rainfall and climate variability had produced years with strong floods or droughts but little in between.
While government schemes and water management strategies had helped reduce salinity, water quality issues such as blue green algae, black water, and hypoxic water events were on the rise, in many cases leading to mass fish deaths.
Native fish populations were under continued pressure, even in areas where environmental water had been returned, according to Matthew Coleman, the authority general manager who led the evaluation.
"There's a lot of other drivers of native fish health," Mr Coleman told AAP.
"So, barriers that don't allow fish to move up and down the river, water quality events and importantly, invasive species like carp - all of these effects are driving native fish health to be poor."
Waterbird populations had improved, but were still recovering from the long-term decline recorded before the Basin Plan was adopted.
As for communities along the river system, the audit found the Basin's economy and its agricultural turnover rose from $35 billion to $54 billion since 2022, but some smaller, less economically diverse towns had faced shrinking populations as their water access dried up.
The evaluation report conceded more must to be done to include Traditional Owners in water management and decision-making, and noted only up to 0.2 per cent of total water allocation by volume was held by First Nations interests.
The authority will hold its annual River Reflections conference in Murray Bridge, South Australia, on July 29 and 30.
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