The findings were among a host of problems identified with controversial flow suspensions imposed on 65 rivers over the past four years. The suspensions were a way to help cope with drought, and saw environmental flows held back in dams to protect drinking water supplies.
But the auditor found the environmental risks of withholding the water were often poorly assessed and monitored, particularly in the Wimmera River in the west and the Tarwin River in South Gippsland.
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The auditor said the Wimmera suspension, managed by Grampians Wimmera Mallee Water, was likely to have damaged the river, and even found that suspension went ahead despite seven times as much water being wasted by antiquated water delivery methods.
''GWMW used open channels to fill farm houses' dams, causing evaporation and seepage losses of around 26,000 million litres,'' the auditor said.
Flows on the Tarwin River were not entirely for protection of human consumption, he said. ''The primary emergency was as much about commercial need as human need.''
Flow suspensions on the Yarra River were imposed to prevent Melbourne going to harsher levels of water restrictions and jobs being lost in the garden and nursery sector, but the auditor questioned the government's claim that 9500 jobs in the garden and nursery industry were being protected.
The auditor praised Melbourne Water for its management of the Yarra flow suspensions.
Environment Victoria's Juliet Le Feuvre welcomed the report and said rivers needed stronger legal protection.
''We can't go on helping ourselves to the rivers' fair share of water whenever the going gets tough,'' she said. ''Our rivers need a guaranteed share of their own water and a modernised Water Act is the way to provide this.''