The warning is in force for Sandside, the harbour and Foreshore road for this afternoon.
A flood warning means flooding is expected and immediate action required,
It has been put in place due to forecast overtopping as a result of very strong winds associated with Storm Ciara driving wave and spray overtopping.
Areas most at risk are properties on Foreshore Road from 4.15pm to 6.45pm on Sunday.
Officials are closely monitoring the situation and have warned residents to be careful along beaches, promenades, coastal footpaths and roads as large waves and sea spray could be dangerous.
If you see someone in trouble on the coast dial 999 and ask for the coastguard.
A yellow weather warning for wind by the Met Office remains in place for Sunday.
Storm Ciara is the third named storm of the 2019/20 winter season, and follows Storm Atiyah, which hit on December 8 to 9, and Storm Brendan, which brought wind and rain to the country on January 13 to 14.
The Met Office say Storm Ciara will bring very strong winds and potentially some disruption to travel throughout Sunday.
Injuries and danger to life from flying debris are possible as well as from large waves and beach material being thrown onto sea fronts, coastal roads and properties.
Some damage to buildings, such as tiles blown from roofs, could also happen.
Road, rail, air and ferry services may be affected, with longer journey times and cancellations possible.
Power cuts may occur, with the potential to affect other services, such as mobile phone coverage.
For an extended forecast click here.