The Drainage and Sewerage Department of the Bangkok Metropolitan Administration (BMA) posted the warning on its website on Saturday.
A message labelled flash news, urged Bangkok residents along Prem Prachakon, Lat Phrao and Prawet Burirom canals to be on alert for flash floods.
Many areas of the city have flooded over the past week following heavy downpours that continued for hours.
The BMA reported a “worrying situation” as water levels in the city’s canals continued to rise following the torrential rain.
City officials manning key floodgates across the city are reportedly struggling to move the water downstream into the sea.
At least three floodgates in the city Klong Song, Saen Saeb, and Lat Krabang reported water volume at critical levels on Saturday morning.
Heavy rain hit Bangkok again on Saturday, with Min Buri district hammered by 100.5mm per hour, Bang Khen by 64mm, Nong Chok by 45.5mm, and Saphan Sung by 42.5mm per hour.