Police intercepted a van while it was transporting the wet plants from a factory that had been flooded in Worksop, Nottingham.
Officers spotted the van speeding at around 10.30pm on Sunday.
Two men fled into nearby fields and officers found the van was packed full of bin bags.
Ten bags containing 25 mature cannabis plants were seized, an amount with a total street value of over £20,000.
The 26-year-old driver was arrested nearby on suspicion of production of cannabis and being concerned in the supply of cannabis, while police are still hunting the second man.
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Following the arrest, the force raided a property on Market Street, Worksop, and found the cellar flooded.
Officers seized one remaining cannabis plant and growing equipment from the attic.
Sergeant Tony Rungay, of Nottinghamshire Police, said: "What started as a relatively routine vehicle stop led to the discovery of a large quantity of drugs.
"The flooding has had a big impact on the town of Worksop, causing misery for a number of families who have had to leave their homes.
“However, it appears it has also had the impact of flushing out some criminal activity by halting some large-scale cannabis production."
Since flooding began last Thursday, around 14,400 properties had been protected by flood defences, including 5,000 in South Yorkshire.
Communities in northern England have been subjected to the torrential conditions, with rain and flooding forcing people to evacuate homes and businesses.