Ms Bligh said the number of people unaccounted for in the Toowoomba area had risen after police took more missing persons reports overnight.
"It's very sad overnight, we've seen even further notifications of missing people," she told the Nine Network's Today program on Wednesday morning.
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"The police now are searching for more than 90 people. These are people who their families can no longer contact or find them.
"It's just a heartbreaking task that they're facing.
"It's a very grim prospect and, as I said, I think very painful day for some families in that region today and a pretty tough day for emergency and search and rescue teams who will really be able to get in there for the first time and I think they're going to find some real devastation."
Ms Bligh said that now the rain had cleared, search crews would move into the area for the grim task to find in what may be one of their toughest days.
"We should all spare a thought for our search and rescue teams," she told Sky News.
"I think they're going to have perhaps one of their toughest days but particularly our hearts are there for those families who, many of them are still holding onto hope and those hopes may well be crushed today as those gruesome finds are possible now that the weather has cleared.
"So, a very, very painful time in that Lockyer valley area."
She said the missing persons toll could grow as people start to look for their neighbours.
Ms Bligh said she was very concerned about people stranded on roofs in the Lockyer Valley after serious flash flooding overnight.
She said rescue teams were trying to pluck them to safety after what must have been a terrifying night.
"We've got people in dire and desperate circumstances. I'm very concerned about those people on roofs," she said.
"I think we're going to be shocked by what we hear out of our search and rescue crews teams today."
Ms Bligh, whose family evacuated her mother to the premier's house overnight, urged people to heed warnings and take the floods seriously.
She said Brisbane homes were expected to flood in significant numbers by Wednesday afternoon, while the Brisbane River flood was expected to peak mid-Thursday afternoon.
Meanwhile, the Ipswich River was expected to rise to 21.5 metres on Wednesday as thousands of people waited out the drama in evacuation centres.
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