Powerful storm Harvey has claimed at least 44 lives and displaced more than a million people on the Gulf Coast.
The Queen said: “I was deeply saddened to learn of the loss of life and the devastation following the recent terrible floods caused by Hurricane Harvey.
“Prince Philip and I send our sincere condolences to the victims of this disaster, to those who have lost loved ones, and to those who have seen their homes and property destroyed.
“My thoughts and prayers are with those affected.”
Harvey hit Texas last week on Friday as a powerful category 4 hurricane, leading to devastating floods in Houston and other areas.
It has since been downgraded to a tropical depression.
US Vice President Mike Pence also visited Texas earlier this week, touring the coastal city of Rockport, where Harvey slammed ashore a week ago.
Outside a damaged church, he said: “The American people are with you. We are here today, we will be here tomorrow and we will be here every day until this city and this state and this region rebuild bigger and better than ever before.”
Around 779,000 Texans have been told to leave their homes and another 980,000 fled voluntarily amid dangers of new flooding from swollen rivers and reservoirs, according to Department of Homeland Security acting secretary Elaine Duke.
The city of Beaumont, about 80 miles east of Houston, had its water supplies cut off and was threatened by a rising river that forced the evacuation of its hospital and residents in neighbouring Orange County.
After Hurricane Harvey, firefighters conducted a house-by-house search in the US energy hub of Houston to rescue stranded survivors and recover bodies as some residents began to return to their homes to assess the damage.
Seventy per cent of Harris County, which encompasses Houston, was covered with 18 inches or more of water, county officials said.
In Beaumont, doctors and nurses evacuated some 190 people from a hospital that halted operations after the storm knocked out water service in the city of almost 120,000 people.
Gasoline futures soared more than 13 per cent earlier this week as almost a quarter of US refining capacity had been knocked offline, raising fears of fuel shortages.
About 189,000 homes and businesses remained without power and nearly 100,000 homes suffered flood damage, utilities and state officials said.