A blockage believed to have caused flooding in a village was the result of woodland cut down by Natural Resources Wales, the body has said.
Pentre in Rhondda Cynon Taff flooded a second time in five days after the culvert collapsed under felled trees.
Rhondda MP Chris Bryant said the damage in the village could cost up to £5m.
Meanwhile firefighters rescued a woman who was clinging to a branch in a fast-flowing river, while another was saved from the roof of a submerged car.
Thursday's yellow warning for rain covered 19 of Wales' 22 local authority areas, with some areas in the north expected to see up to 100mm (4in) of rain.
NRW said engineers had been checking flood defences and carrying out urgent repairs and clearing blockages.
However Mr Bryant said the government-sponsored body had "questions to answer" for not keeping culverts clear and should set up a multi-million pound compensation fund.
His comments followed flooding in Pleasant Street, Pentre, following the collapsed culvert.
Residents called the situation "horrific" and said houses had suffered severe damage.
NRW confirmed 95% of the Pentre woodland had been felled in a bid to tackle Larch disease.
Bill Purvis, NRW duty tactical manger, said: "From the photographs and pictures available it is evident that wooded material entered the watercourse and ended up blocking the grid.
"A review will be undertaken of our operations so that we learn lessons and can make improvements to ensure this doesn't happen again."
Forecasters had predicted a month's rain could fall in north Wales over 24 hours and the fire service warned people not to drive through floodwater.
Twenty firefighters from Mid and West Wales fire service rescued a woman clinging to a branch near Brecon promenade, Powys, at 03:00 GMT on Thursday.
The Welsh Ambulance Service said she was taken to hospital.
A second woman was also rescued from the roof of a submerged car on the Wales/England border near Chepstow on Tuesday, fire chiefs confirmed.
Mark Smith, 51, told the BBC's Victoria Derbyshire show how he waded into floodwater on the banks of the River Wye to rescue the woman who had been trapped for 12 hours near St Briavels in the Forest of Dean.
Some Rhondda Cynon Taf council staff were moved out of their offices at Clydach Vale amid concerns of a potential landslide nearby, but have since returned.
The authority said it was also drawing up plans to rebuild a damaged wall on the River Rhondda at Blaencwm.
Leader Andrew Morgan said up to 1,000 properties had been affected by flooding and 20 families were being housed in temporary accommodation.
"On top of that we had massive damage to infrastructure. At least three possibly four bridges will need to be completely replaced," he added.
In Bridgend, council engineers were checking 41 former coal mining sites in the Ogmore, Garw and Llynfi valleys to ensure they are safe.
The Coal Authority confirmed it was also checking sites they might have responsibility for.
Residents in Ynysybwl have complained that sandbags delivered on Thursday were too little, too late.
Paul Thomas lives on Clydach Terrace where 19 houses were flooded on Saturday night by water that was "over head height".
"Outlying areas like ours don't get the money or support and we've only now been given sandbags," he said.
"However the level of water exceeded the four sandbags we got by about five feet, so they would have been a total waste of time anyway."
The political fall-out
Labour leader Jeremy Corbyn visited Rhydyfelin in Pontypridd on Thursday and criticised the UK government's response as "wholly inadequate".
Mr Corbyn said Boris Johnson was showing his "true colours", adding: "If the prime minister is not campaigning for votes in a general election he simply does not care about helping communities affected by flooding."
Plaid Cymru leader Adam Price also questioned why Mr Johnson had not convened Cobra, the UK government's emergency response committee.
In response, a UK government spokesman said flood defences and the response to flooding were devolved to the Welsh Government.
"The UK government has communicated with emergency services, local authorities and the Welsh Government - including the first minister - throughout the past week and we are ready to provide assistance, where possible, should additional help be required," he said.
A Welsh Government summit was held on Wednesday with councils and other agencies to look at the problems caused by flooding.
First Minister Mark Drakeford told BBC Breakfast: "This is a genuine emergency and we are working to mobilise every bit of help we can for families."
Meanwhile, the Plaid Cymru leader of Carmarthenshire council has accused the Welsh Government of "favouritism" when it comes to dealing with the aftermath of flooding.
Emlyn Dole told Newyddion 9 the Labour-led Welsh Government had "reacted in the areas that they are strongest".
He added: "So far there has been no reaction to what happened with Storm Callum 18 months ago, whilst there has been a reaction straightaway to what has happened this time.
"Our people had the same serious situation last time - but there wasn't a penny to help."
A Welsh Government spokesman said the impact and severity of storms Ciara and Dennis had been unprecedented, adding: "We will always ensure we do everything we can to support everyone affected."
Prince Charles, the Prince of Wales, is due to visit Pontypridd on Friday to speak to home owners forced to leave their properties and the rescuers who saved many from rising waters.
And Hollywood actor Michael Sheen, from Port Talbot, has launched a crowdfunding campaign to help flooded communities.
"The devastation that Storm Dennis has left behind is very real and thousands of people across the UK have lost everything," he said.
The Welsh Rugby Union has also set up a fund to help rugby clubs affected by the weather.
Water bottle stations were set up in Monmouth after fears hundreds of homes could be left without supply after Welsh Water's treatment site was flooded.
Managing director Peter Perry said it could take up to 48 hours to get the Mayhill plant up and running.
South Wales Fire and Rescue Service have warned of the potential dangers of carbon monoxide poisoning from using gas-powered power generators during the clean-up.
Network Rail has reopened the Treherbert line, Heart of Wales line and the Cambrian lines, however the following lines remain closed:
- Ebbw Vale Line (north of Cross Keys)
- Abergavenny to Hereford
- Valleys Aberdare line
- Conwy Valley line
'Dirt, damage and despair'
BBC reporter Nicky Smith reports from Treforest
I have spent time at Treforest Industrial Estate and what I witnessed was dirt, damage and despair.
In the businesses I spoke to, they are only just beginning to understand the financial cost of Storm Dennis and, in each one I stopped at, they talked of it running to thousands of pounds.
But in all the mess, there is one very clear message. They will do everything in their power to stay open for business.
Harry Singh, who owns the Welsh Shop which stores its stock here, showed me piles of merchandise ruined by the flood water - he believes he has lost up to £400,000 worth of stock.
The impact is even worse as this is one of their busiest times, in the middle of the Six Nations rugby championship, and he has not been able to fulfil online orders.
A couple whose home was damaged and a roof was swept into their garden during the floods, told me they would not be able to return home for up to 18 months.
Paul Cooper said they felt a bit lost following the news and, like many others, hoped for good news soon.
'It could be months before people can go home'
BBC reporter Matt Murray in Pontypridd and Nantgarw
Roads are now crowded with skips, tractors and trailers clearing debris, rubbish, and cars that have been written off.
There's a realisation by those affected just how life-changing this will be for them.
Self-employed builder Lynn Davies had just finished refurbishing his home when it was flooded and all his tools and van, which he needs to work, were also ruined.
He is now living in a hotel with his family and dogs and says it may be five months before they can return home.
There's also anger here as people feel they were alerted too late to the risk of the flood waters hitting their homes.
'Community spirit in action'
BBC reporter Rhys Williams in Ystradgynlais
The Teddy Bear Bridge - so-called because miners teetering across the previous rickety bridge to get to work looked like teddy bears - is one of the victims of the heavy rain in Ystradgynlais.
The more modern bridge is still standing, but there's a huge crack in the wall and the structure has buckled considerably.
The storm has also caused flooding for residents in Ystalyfera, where the community is banding together and reminding people of the "good old days" when everyone pitched in together to help out.
On Wednesday residents were in their third day of clearing out the downstairs of their homes into bags to be collected by the council.
Lenny Jenkins has spent the day clearing out his home, ruined by the water. Like the rest of his street, he says has no insurance as no company will "go near us."
Most of his neighbours have been re-housed by the council. He's worried the community in the area is going to suffer as people leave the street.
- Natural Resources Wales
- Merthyr Tydfil
- Michael Sheen
- Carmarthenshire County Council
- Adam Price
- Jeremy Corbyn
- Met Office
- Prince Charles, Prince of Wales
- Storm Dennis
- Severe weather
- Welsh government
- Port Talbot