All buildings along the promenade in Aberystwyth have been evacuated as further high tides and an "exceptional" wave swell are expected later.
Residents were warned to vacate properties as soon as possible and use a nearby support centre that has been provided.
About 150 students in seafront flats have been moved out and will not return until safety checks are carried out.
High tides and strong winds battered parts of Wales for a fourth day.
Seven flood warnings and eight flood alerts were in place on Monday evening.
On Anglesey, a detached cottage in Llanfachraeth, near Holyhead, has been destroyed by fire after it was struck by lightning.
The fire is thought to have started in the roof and spread throughout the building as flames were fanned by high winds. No one was injured.
Around Wales, two yellow weather warnings - meaning be aware - are in force, one for rain and another for wind.
Ceredigion council is "strongly advising" all residents to evacuate properties along the promenade in Aberystwyth after Natural Resources Wales (NRW) warned of a wave swell at 23:37 GMT.
The council said: "In light of the existing damage this could cause serious injury, substantial flooding and damage to properties."
A support centre has been set up in Plascrug Leisure Centre.
The Aberystwyth student residence is to remain closed all evening while the building is assessed.
Students who have not yet returned to Aberystwyth after the Christmas holidays and who live on the seafront have been asked by the university to stay away.
The town's seafront shelter has partially collapsed into the pavement following the buffeting from the waves.
Dyfed-Powys Police tweeted it had closed a number of roads in Amroth, Newgale, Aberystwyth and Borth. Drivers were advised to avoid coastal areas and not attempt to drive through flood water.
Mid and West Wales Fire Service said they were attending flooding at properties in Borth.
In Capel Curig in Conwy, gusts of 70mph were recorded on Monday at 08:00 GMT.
A gust of 66mph was recorded at Aberdaron on the Llyn Peninsula and another of 56mph at Mumbles at 10:00 GMT.
Earlier 17 alerts of possible flooding were issued which have dropped to just eight by mid-afternoon.
It came as councils along the coast of Wales assessed the damage caused by Friday's exceptional storm surge.
Minister Alun Davies said there would be "no blank cheque" for rebuilding the promenade but said emergency funding would be available and urged Ceredigion council to apply.
He previously said he had been "shocked to the core" at damage in Aberystwyth and ordered a review of coastal defences.
The promenade was hit by a tidal surge on Friday evening and the storm brought rocks and debris onto the front and nearby streets after high tide.
NRW is updating its website every 15 minutes and the Environment Agency has a live flood warning map on its site.
People who live in areas at risk of flooding can register for free flood warnings by calling Floodline on 0845 988 11 88.
As well as the risk of flooding, transport networks were affected across Wales on Monday.
There were speed restrictions on the M48 Severn Bridge and the Britannia Bridge in north Wales due to high winds.
In Pembrokeshire, the Cleddau Bridge has been closed to high-sided vehicles and the A487 is shut between Welsh Road (Newgale) and Anchor Down (Solva).
On the railways, there was disruption on several Arriva Trains Wales services due to flooding.
Buses will replace trains from Llandudno Junction to Blaenau Ffestiniog until further notice, while the line between Machynlleth and Pwllheli will remain closed for several weeks due to extensive damage.
A replacement bus service is running between Llanelli and Carmarthen due to obstructions on the line at Pembrey and Burry Port.
All sailings are cancelled on Stena Line between Fishguard and Rosslare.
There will be full coverage of disruption from the stormy weather and flooding on BBC Wales online, via Twitter @BBCWalesNews, on Wales Today bulletins on BBC One Wales and on BBC Radio Wales.