Construction of tunnels for the North East Link could cause "stress and degradation" to parts of the Yarra River and its tributaries, the Andrews government has conceded.

And at least two creeks are in danger of becoming concrete drains in sections because of the road works.

The potential impact of the toll road has been revealed for the first time in documents filed by the Andrews government with the federal environmental department.

The North East Link is the most expensive toll road project Victoria has ever embarked on, at an expected cost of $16.5 billion.