During heavy rain last month, part of the river merged into adjacent Caistron Lakes, near Rothbury.
This bank has now naturally breached meaning most of the River Coquet is now flowing through the lakes area.
Its new course meant a 500m stretch of the original channel was left depleted.
Environment Agency fisheries specialists have been relocating fish in this cut off stretch of river to ensure their survival.
Over 250 fish have been rescued and returned to the main river, including juvenile salmon, trout and lampreys.
Experts are also working with Natural England to monitor the new course and any environmental impact.
The natural phenomenon, which has not led to any increased flood risk, had been expected and prepared for by the Environment Agency and its partners.
Stephen Merrett, flood risk operations manager for the Environment Agency in the North East, said: “We’ve been closely monitoring the River Coquet over recent years and together with partners developed an incident response plan to reduce the impact on the community and environment.
“The bank holding the impounded water has now breached, and as expected, the river has taken a new course. The River Coquet is a naturally wandering river and erosion, switching channels or the formation of new channels is an entirely normal occurrence.
“It’s a protected conservation area and so allowing this natural process to take place ensures it remains a good habitat for wildlife and environmental features.”
A 2019 meeting involving agencies including the Environment Agency, Northumberland Rivers Trust, Natural England, and landowner, fisheries and Northumberland County Council representatives, discussed the potential issues with the River Coquet and the likely future breach.
Caistron Lakes were created many years ago when the River Coquet overtopped into a sand and gravel extraction site.
The Environment Agency had worked with Northumberland County Council to put in place additional flood risk measures in Rothbury – such as closing footpaths and car parks – should the bank breach during high river levels. These have been removed.