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Heavy flooding has become nearly an annual rite of passage in the practically sea-level city, where experts have long warned of the potential for catastrophe.
"I regret anyone whose home is flooded again," said city mayor Sylvester Turner.
"There's nothing I can say that's going to ease your frustration. We certainly can't control the weather," he said.
"A lot of rain coming in a very short period of time, there's nothing you can do," he added.
Flash flooding and more rain is possible a day after some areas saw water levels approaching 20in.
Scores of subdivisions flooded, schools were closed and power was knocked out to thousands of residents who were urged to shelter in place.
In addition to its location, Houston's "gumbo" soft soil, fast-growing population and building boom that has turned empty pastures into housing developments all over the city's suburbs make it vulnerable to high waters, experts say.
Harris County, where Houston and many of its suburbs are located, has seen a 30% jump in population since 2000. Its surrounding counties have almost grown more than 10% since 2000, according to the Greater Houston Partnership, a business group.
Some of the resulting developments include adequate green space for water runoff, but not all of them do, said Philip Bedient, an engineering professor at Rice University.
"Could we have engineered our way out of this? Only if we started talking about alterations 35 or 40 years ago," Mr Bedient said.
Samuel Brody, director of the environmental planning and sustainability research unit at Texas A&M University, last year called Houston "the number one city in America to be injured and die in a flood".
Rainstorms last May caused major flooding that required authorities to rescue 20 people, most of them drivers, from high water. Drivers abandoned at least 2,500 vehicles, and more than 1,000 homes were damaged in the rain.
The year before, flash flooding in Houston and suburban counties left cars trapped on major highways.
Those storms still pale in comparison to the devastation wreaked by Hurricane Ike in 2008 and Tropical Storm Allison in 2001. Allison left behind five billion dollars (£3.4 billion) in damages and flooded parts of the city centre and the Texas Medical Centre, which sits near the Brays Bayou, a key watershed.
Mr Bedient has worked with the Texas Medical Centre on better preparing its facilities for massive rainfall, including the use of a sophisticated weather alert system that gives the centre extra time to activate gates and doors that block excess rainwater.
Improving the monitoring of specific watersheds and flood-prone areas might give affected residents the extra bit of time they need to save lives and take protective measures, he said.
"We can't solve this flood problem in Houston," Mr Bedient said. "All we can do is a better job warning (people)."