The 33-year-old man was last seen fishing off the rocks at Tangle-Ha, a remote village near St Cyrus in Aberdeenshire.
He was reported missing at around 3am yesterday when another angler raised the alarm.
Conditions in the area have been described as "exceedingly rough" with large sea swells of up to 10ft being reported.
Earlier, the local coastguard dispatched a search party to scour the coastline.
A rescue helicopter and a lifeboat from Montrose also assisted with the search.
After carrying out an initial search, the teams found no trace of the missing fisherman and all parties were stood down.
However, the coastguard launched a second search throughout the area late last night.
Kevin Brown, watch manager at Aberdeen coastguard, said: "A search is still ongoing to find this missing sea angler.
"We'd always recommend anglers check weather and tides before setting out and make sure they wear suitable clothing and a lifejacket. If you get into difficulty, or spot someone else in trouble, call 999 straight away and ask for the Coastguard."
The rescue effort is expected to continue through the night but will likely be hampered by forecasted high winds of 40-45mph.
Further rainfall is expected early tomorrow across Scotland.
There was also widespread flooding in the Borders and Dumfries and Galloway, with Dumfries again badly affected.
The Solway Firth communities of Dalbeattie, Kirkcudbright and Rockcliffe were all heavily affected while the centre of Stornoway remained under water yesterday.
Flood warnings are also in place in with the River Earn, from Perth to Crieff, in danger of bursting its banks.
The vast majority of the country remains under flood alert.
In England, severe flood warnings are in place on the Severn estuary and along coastal areas from Land's End and Plymouth.