The Environment Agency said flooding is expected in two areas of the county – Barcombe Mills on the River Ouse, north of Lewes, and at Hellingly and Horsebridge on the Cuckmere and Bull Rivers, near Hailsham.
In Barcombe Mills, The Anchor Inn, fields and gardens are expected to flood, with Anchor Lane and Barcombe Mills Road “likely to be impassable”.
People living nearby have been advised to activate flood protection products.
In Hellingly, the Environment Agency said flooding will affect properties in Mill Lane, as well as Grove Hill near Grovebridge Farm and Hammer Lane near Cowbeech.
From 2pm, flooding will also affect properties in Station Road, Church Lane and Church Road, as well as the roads, fields and gardens.
A further 22 flood alerts have been issued across West and East Sussex, meaning flooding is possible.
A yellow weather warning for heavy rain has been issued in Sussex as Storm Chandra hits the county.
The flood alerts are in place at:
Bridge Road, Emsworth
Lower Arun
Lower River Ems
River Adur East Branch
River Adur West Branch
River Lox
River Mole and its tributaries from Kinnersley Manor to South Hersham
Rivers Eden and Eden Brook
River Uck
Tilmore Brook Petersfield
Upper Arun
Upper Ouse
Upper River Medway
Upper River Mole, Ifield Brook, Gatwick Stream and Burstow Stream
Upper River Wey
Western Rother
Combe Haven
Cuckmere River
Langney Haven
Polegate and Wannock
Rivers Tillingham and Brede
Upper River Stour