Images shared by the local authority show rubble scattered around areas near the seafront.
The town’s flood defences were praised in October last year after holding firm against the rising River Carron during torrential rainfall.
Sepa said a “combination of high tides and prevailing weather conditions” was to blame.
The watchdog added: “Flooding from the sea is expected to affect low lying land, roads and properties along the coast in Stonehaven.
“Wave overtopping is expected around Cowie Promenade.
“There is a risk of flooding from waves and spray overtopping to low lying areas of the coast, from Friday evening until Sunday morning.”
