They were being transferred from Greenstone municipality, which is housing almost 200 evacuees, because of a lack of hotel capacity.
On Sunday, Greenstone mayor Ron Beaulieu told CBC News the evacuees were staying in the Geraldton arena.
Officials said they weren't certain how many were coming to Thunder Bay, but expected the number to be fewer than 100.
The new arrivals will join the 155 Attawapiskat evacuees staying at the Valhalla Inn in Thunder Bay.
Emergency Management Ontario estimates about 400 people in total have been flown to Thunder Bay, Greenstone and Fort Frances due to fears the Attawapiskat River will flood the community. Some people's homes have already been damaged by sewage.
Thunder Bay Deputy Fire Chief David Paxton said in addition to providing the basics of shelter, food and medical care, the city and other agencies are organizing recreational activities for the evacuees.
"[On Sunday] we took them on a bus tour and they filled the capacity of the buses within five minutes," he said. "They were quite excited just to get out and see a little bit of the area. For some this is their first trip to Thunder Bay."
Pic Mobert First Nation also under flood threat
Pic Mobert First Nation, located about 270 km north of Sault Ste. Marie, has declared a state of emergency due to rising water levels on the White River. Sandbags have been placed near several homes in the community where the danger is the greatest, to try to protect them.
About 15 evacuees from that community arrived in Geraldton on Saturday and were staying in hotels, according to Beaulieu.
But on Monday, Emergency Management Ontario said they would be taken by bus to Sault Ste. Marie, which has agreed to host all Pic Mobert evacuees.
The Ministry of Natural Resources said flooding will remain a threat until the 30 cm-deep snowpack in the White River watershed has melted.
The ministry said the thaw over the next few days would likely be compounded by two to four millimetres of rain.
Attawapiskat and Pic Mobert First Nations are the latest northern Ontario communities to fly residents out because of flooding danger.
Last week, Kashechewan First Nation sent its most vulnerable residents, including the elderly, families with small children and people with medical conditions, to Thunder Bay, Geraldton and Longlac. They returned home Friday, after Kashechewan leaders deemed conditions there to be safe.Suggest a correction