Several communities in both provinces have declared states of emergency.
Firefighters went door-to-door in Gainsborough, Sask., on Sunday night advising everyone to leave after water rose on the last available road out of the village.
The mayor of Gainsborough says dozens of homes and businesses were flooded and that it was "going to be a disaster."
WestJet had cancelled flights in and out of Brandon, Man., when water swamped the road into the terminal north of the city. But city spokeswoman Allison Collins said Monday that travellers heading to Calgary on the afternoon flight can get to the airport by taking a detour.
The Saskatchewan government is sending flood-control teams to areas that include Yorkton, Melville, Esterhazy, Redvers and Carlyle.
Regina's fire department tweeted last night that the city's sewage system was working at full capacity, and it asked residents to delay showers, baths and even flushing toilets to prevent additional strain on the system.
In nearby Melville, rain overwhelmed the city's storm and domestic sewer systems on Monday morning.
Kris Carley, the emergency measures operations co-ordinator for the town of Carnduff and the rural municipality of Mount Pleasant, said flooding in the area was getting worse. He said the community is functioning, but roads are getting cut off and people could be stranded.
"There's not a lot we can do," said Carley. "Mother Nature's got us and we just have to try to react."