The monarch sent a message of solidarity to Pakistan as the southern Sindh province braced for another deluge from swollen rivers in the north.
As the death toll from this year's monsoon reached 1,033 on Sunday, the queen reached out to Pakistan's President Arif Alvi with a message of sympathy.
“I am deeply saddened to hear of the tragic loss of life and destruction caused by the floods across Pakistan,” the queen said.
“My thoughts are with all those who have been affected, as well as those working in difficult circumstances to support the recovery efforts.
“The United Kingdom stands in solidarity with Pakistan as you recover from these terrible events.”
The message, released by Buckingham Palace, was signed “Elizabeth R”.
The Indus River that flows through Pakistan's second-most populous region is fed by dozens of mountain tributaries to the north, many of which have burst their banks following record rains and glacier melt.
Officials said torrents of water were expected to reach Sindh in the next few days, bringing more misery to millions affected by the floods.
“Right now, Indus is in high flood,” said Aziz Soomro, the supervisor of a barrage that regulates the river's flow near the city of Sukkur.
Authorities said the devastation is worse than in 2010, when 1,700 people were killed by floods.
Qamar Javed Bajwa, current Chief of the Army Staff in Pakistan, said on Sunday that the country may take years to recover.
International aid agencies are providing emergency relief and on Saturday, President Sheikh Mohamed said the UAE would send 3,000 tonnes of food and medical supplies.
The UK also said it had contributed £1.5 million ($1.7m) towards aid efforts.
Pakistan’s military chief, Gen Qamar Javed Bajwa, appealed to the international community for more help.
“The federal government, provincial governments and armed forces resources are limited. Come forward, in any way you want to help, donating financially or [with] relief goods,” Gen Bajwa said.
“Friendly countries will also come forward to help Pakistan in this hour of need.
“I also appeal … to our expats and our friends abroad, to please come forward and help these people who in are in a very, very difficult situation.
“I am sure our expats as usual will not disappoint their brothers back home in Pakistan,” he said.
The annual monsoon is essential for irrigating crops and replenishing lakes and dams across the Indian subcontinent, but it also brings destruction.
Monsoon flooding this year has affected more than 33 million people, about one in seven Pakistanis, destroying or damaging nearly a million homes.
On Sunday, Pakistan's National Disaster Management Authority said the death toll from the monsoon rains had reached 1,033, with 119 killed in the previous 24 hours.
In parts of Sindh, the only areas of dry land are elevated roads and railway tracks, along which tens of thousands of rural poor have taken shelter with their livestock.
Near Sukkur, a row of tents stretched for two kilometres, with people still arriving by boats loaded with cots and cooking utensils — the only possessions they could salvage.
“Water started rising in the river from yesterday, inundating all the villages and forcing us to flee,” labourer Wakeel Ahmed, 22, told AFP.
Prime Minister Shehbaz Sharif, who cancelled a trip to Britain to oversee relief operations, said he had never seen anything like it before.
“Village after village has been wiped out. Millions of houses have been destroyed. There has been immense destruction,” Mr Sharif said, after flying over Sindh by helicopter.
He was scheduled to visit the neighbouring province of Balochistan, which has also suffered widespread flooding, on Sunday.
The disaster could not come at a worse time for Pakistan as it struggles with an economic crisis and political turmoil after the removal of former prime minister Imran Khan by a parliamentary vote of no confidence in April.
Sherry Rehman, Pakistan's Minister for Climate Change, said the country was experiencing a “serious climate catastrophe, one of the hardest in the decade”.
“We are at the moment at the ground zero of the front line of extreme weather events, in an unrelenting cascade of heatwaves, forest fires, flash floods, multiple glacial lake outbursts, flood events — and now the monster monsoon of the decade is wreaking non-stop havoc throughout the country,” she said in a video posted on Twitter.
Flooding from the Swat River overnight affected the northern Khyber Pakhtunkhwa province, where tens of thousands of people — especially in the Charsadda and Nowshera districts — have been evacuated from their homes to relief camps set up in government buildings.
Many have also taken shelter on roadsides, said Kamran Bangash, a spokesman for the provincial government.
Mr Bangash said about 180,000 people have been moved to safety from Charsadda and 150,000 from Nowshera district villages.
Khaista Rehman, 55, was sheltering with his wife and three children along the Islamabad-Peshawar motorway after his home in Charsadda was submerged overnight.
“Thank God we are safe now on this road quite high from the flooded area,” Mr Rehman said.
“Our crops are gone and our home is destroyed, but I am grateful to Allah that we are alive and I will restart life with my sons.”
The unprecedented monsoon season has affected all four of the country’s provinces.
Almost 300,000 homes have been destroyed, numerous roads rendered impassable and power cuts have been widespread, affecting millions of people.
Pope Francis on Sunday said he wanted to assure his “closeness to the populations of Pakistan struck by flooding of disastrous proportions”.
Speaking during a pilgrimage to the Italian town of L’Aquila, which was hit by a deadly earthquake in 2009, the Pope said he was praying “for the many victims, for the injured and the evacuated, and so that international solidarity will be prompt and generous”.
Mr Rehman told Turkish news outlet TRT World that by the time the rains recede, “we could well have one fourth or one third of Pakistan under water”.
“This is something that is a global crisis and, of course, we will need better planning and sustainable development on the ground … We’ll need to have climate resilient crops as well as structures,” he said.
With reporting from AFP and AP.