The Yarra, Murray, Snowy, Wimmera, Glenelg, Thomson and Loddon rivers are among those suspected of not receiving their legal entitlements.

The audit, commissioned by Environment Victoria, raised doubts about whether the Government was meeting its legal obligations and recommended an overhaul of the way water is shared among irrigators, industry, domestic users and the environment.

The report found that a lack of openness, clarity, proper monitoring and public access to information made it impossible to determine precisely how much water was being diverted away from the environment and where it was going.

The audit found 80 per cent of Victoria's rivers and tributaries were in poor or very poor condition and highlighted inconsistencies in Government data on river levels, stream flows and releases from water storages.

It also questioned whether Victoria was honouring commitments to the National Water Initiative that binds all states, territories and the Commonwealth to minimum environmental provisions and comprehensive monitoring systems.

"The Yarra and Thomson have had environmental flow promises, but they have never been delivered," said Healthy Rivers campaigner Juliet Le Feuvre.

"The current algal bloom in the Murray highlights what can happen when there are not enough environmental releases to flush the system."

The Government established the Environmental Water Reserve in 2005 to "preserve the environmental values and health of water ecosystems".

But in 2007 the Minister for Environment was granted discretionary powers to "qualify" environmental entitlements so that water could be redirected to irrigators, industry or domestic users.

The Environment Victoria audit criticised the lack of transparency on those ministerial qualifications.

"More clarification is needed by the Victorian Government to ensure that the amount of water the environment is legally entitled to … is supported by rigorous monitoring activities and clear penalties for compliance failure," the report said.

It warned that the long-term health and viability of the Yarra River was at risk from insufficient passing flows, and said the Government refused to release data on environmental flows to the Snowy River.