At least a dozen schools in the provinces of Yala and Narathiwat have been forced to close, while footage from the region showed homes and shops inundated with murky brown waters and residents taking refuge on upper floors.
The heavy rains have also caused problems at sea, with at least seven boats sunk in the Gulf of Thailand and Andaman Sea since Friday.
The kingdom's state railway company said track subsidence meant that trains heading south to the Malaysian border were stopping at Yala, 100 km away.
Authorities have warned residents in the provinces to be ready to evacuate if the floods get worse.
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