The Environment Agency has told people to "be prepared" for flooding in low lying land, roads and riverside areas near the A12.
The alert has been put in place for areas around the River Colne near Colchester.
The warning says: "Areas most at risk are low-lying land in Colchester between the A12 and East Street.
"Take care on riverside footpaths and don't put yourself in unnecessary danger."
The alert is currently in place and the Environment Agency has said it will reassess the situation at 6pm this evening.
A yellow weather warning was issued on Sunday, September 19 for the region, with torrential downpours causing one road in a Suffolk village to become "impassable".
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