In parts of Halton in Leeds, the flood warning has been raised to red.
A message on the UK government website states: "River levels have risen as a result of persistent heavy rainfall overnight and this morning, 09/02/20, due to Storm Ciara.
"The siren has been sounded. "
Dale Bowes, 24, took video footage of the siren and sent it to The Yorkshire Evening Post.He said it sounded across the area for up to two minutes.
The message on the website continued: "We expect river levels to continue to rise until the early afternoon today, when the rain is forecast to ease into a pattern of showers.
"To report property flooding please call 0800 80 70 60.
"We are closely monitoring the situation from our incident room.
"Please put your flood plan into action and see GOV.UK for a 5 day flood forecast."
Meanwhile, in Scotland, Rail and ferry services in Scotland were disrupted as Storm Ciara brought heavy wind and rain to the UK.
Authorities had already warned the storm was likely to cause "significant disruption" after the Met Office issued yellow warnings of strong winds across Scotland on Sunday with gusts of up to 80mph possible in some areas.
Heavy rain resulted in flooding in the Whitesands area of Dumfries, after the River Nith burst its banks.
This story first featured on our sister site the Yorkshire Evening Post.