The Lemonade star said: "I remain in constant prayer for those affected and for the rescuers who have been so brave and determined to do so much to help."
She said that she was working with her charity and her pastor to "implement a plan to help", and posted an Instagram tribute telling residents they were in her prayers.
Beyonce, who grew up in the city's Third Ward, has often referred to her home in her work, including in songs "Run The World (Girls)", "Flawless" and "Formation".
Many celebrities have come forward to help with relief efforts as Houston battles unprecedented levels of rain, with at least nine killed in the storm.
Coldplay, who had to postpone their concert in Houston last week due to the hurricane, wrote a song for those affected by the floods and debuted the track in Miami.
Officials estimate that more than 30,000 residents need shelter.
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