North Wales Fire and Rescue Service says it had around 250 calls for flooding overnight mainly on Anglesey and in Gwynedd.
The former Plas Arthur Leisure Centre was opened as a shelter. The A55 is still closed on Anglesey and part of the A5 was also closed.
Train services between Llandudno Junction and Blaenau Ffestiniog and between Bangor and Holyhead are suspended. There are replacement bus services but Arriva Trains Wales says they may not get through because of the flooding.
There are 4 flood warnings in force; River Rhyd Hir at Riverside Terrace, River Adda at Bangor, River Erch at Abererch and Conwy Valley.
A Met Office 'be aware' alert is in force until 9am.
Capel Curig in Snowdonia topped the UK's wildest weather chart overnight.
The Met Office says 89mm (3.5 ins) of rain fell and there were gusts of up to 84mph.
Here is a list of road closures after last night's flooding:
A5 Fford Bangor (Bangor Road) between Bethesda and Pont Pen-y-benglog.
A545 Ffordd Beaumaris (Beaumaris Road) is closed in both directions because of a landslip between Lon Bryn Teg (Bryn Teg Lane) and B5420 Cil-Bedlam (Dale Street) / Ffordd Y Paced Water Street.
A55 is closed between J6 A5 / A5114 (Llangefni) and J7A A5 (Llanfair P.G. West).
A4085 is closed because of flooding between the B4418 (Rhyd-ddu) and Ffordd Eryri (Waunfaw
A4086 is closed in both directions because of flooding at Nant Peris.
A4087 in both directions between the A487 / B4547 (Y Felinheli Roundabout) and Lon Cytir (Cytir Lane).
A5025 Southbound at Pentraeth between the B5109 and B5420 (Four Crosses).