They said that flooding in and around low lying parts of Fraserburgh is possible.
In addition, a warning has been published for Stonehaven.
Sepa said that a combination of high tides and bad weather conditions means that flooding from the sea is expected to affect low-lying parts of the coast.
Wave overtopping could result in flooding in Cowie, and in particular Boatie Row.
This warning is for tomorrow between 1.30am and 1.30pm.
A flood alert has also been issued for Aberdeen between 20 past midnight and 12.45pm tomorrow.
Parts of the Western Isles have also been included in a flood warning.
Sepa said that coastal flooding is expected in Stornoway, Baleshare and between Ardmore and Loch Carnan from 6pm this evening.
