The project on the River Nar aims to restore pools, meanders and gravel areas in the channel and reed beds.
Dilapidated weirs will be removed to allow more dynamic flows and reduce the build up of silt in the river.
Norfolk Rivers Board, the Environment Agency, Natural England and landowners will begin work on Monday at Castle Acre, Narborough and West Lexham.
The aim is to recreate habitat where eels, brown trout and sea trout as well as water voles, rare dragonflies and otters can thrive.
Most of the River Nar is protected as a Site of Special Scientific Interest (SSSI) status.
Chris Bell, technical officer for the Environment Agency, said: "Over the generations there has been significant deterioration to some areas of the river.
"But I am delighted that we are now at the beginning of a focused effort to reverse this decline and bring life back to the whole of the river."
Work to restore a Norfolk river to a more natural state is starting next week at three sites.