The carriageway has been shut eastbound at Bradford Peverell between the A37 and the A354 Weymouth Relief Road.
The road is submerged in water for a distance of 50m (165ft), Dorset Police said.
Police urged motorists to avoid the area as the section of road road was likely to remain closed for several hours.
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The force said the westbound carriageway remained open with only a small amount of surface water, but urged motorists to take extra care.
A stretch of the A35 near Dorchester been closed because of deep floodwater on the road.