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Faversham Creek has burst its banks following a large tidal surge.
Floodgates have also been closed in Herne Bay and Whitstable, while officers are operating sluice gates at coastal brooks to stop the sea coming inland.
A wind-driven surge has caused the usual high tide to be higher than predicted.
Several flood alerts are in place in Kent, with one reaching from Gravesend to Sittingbourne, and another from Margate to Dover.
As is usual with extreme high tides, Faversham's Creek has spilled water onto surrounding roads including Conduit Street.
Barriers have been put outside The Quay restaurant in an effort to prevent water coming into the premises.
The chance of flooding at coastal and creekside areas is expected to continue until after the high tides at 12.45pm tomorrow.
A statement published yesterday by Canterbury City Council in anticipation of the high tide, reads: "Some floodgates will remain open but this doesn't mean we have forgotten to close them.
"The forecast will be monitored very closely and if necessary, we will close further floodgates along our seafront.
"Our staff will be out monitoring the high tide and operating sluice gates at coastal brooks to stop the sea coming inland."
High tide along the north east coast of Kent came at about 2pm today.
A spokesman from the Environment Agency said: "We expect flooding to affect coastal areas, particularly low-lying land and roads nearest the sea.
"We are closely monitoring the situation and our incident response staff are prepared to respond if required."