The £475,000 project aims to reduce the risk of flooding to around 1,000 homes at Chapel Beck in Guisborough, Cocker Beck in Darlington, and Loftus Beck in Loftus.
Contractors will carry out repairs and remove blockages and silt build-up deposits.
The work began on 18 January will be completed by the end of February.
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Further cleaning and repairs will be carried out at:
• Dene Beck, South Church, Durham.
• Woodlea, Forest Hall, North Tyneside.
• Alnmouth Terrace, Acomb, Northumberland.
• Smallhope Burn, Lanchester, Durham.
• West Beck, West Auckland, Darlington.
These works will begin in February and be completed during April.
The Environment Agency's Steve Wilkinson said: "The build-up of silt in culverts reduces the capacity for water to pass through, particularly when it's needed most during a flood.
"This in turn can raise water levels further upstream which can lead to flooding. As well as clearing silt, the work will see lodged debris in the culverts, such as logs and tyres, removed. This will reduce the risk of flooding to nearby homes and businesses."
(LM)
