The dead were on two overcrowded rescue boats that capsized while ferrying people to relief camps and included children washed away by strong currents, said Bihar state's disaster management secretary Prataya Amrit.
The boats were carrying people away from flooding caused when the Kosi river breached its banks in Nepal and changed course, inundating Bihar.
'These were areas that rescue teams had been struggling to reach and evacuate people,' Mr Amrit said.
The death toll of nearly 100 was likely to rise as many areas were still inaccessible, officials said.
Rescuers had evacuated more than 550,000 people to safety with about 200,000 of them sheltered in relief camps, Mr Amrit said.
Bihar chief minister Nitish Kumar, who on Monday toured submerged districts, said there was little chance of the floods receding for at least a month. -- AFP