157 patients from the Melville and District Health Centre and St. Paul's care home were being move to the Horizon Credit Union Centre, a hockey rink.
People started the transfer shortly before 6 a.m. CST.
Volunteers have been working through the night filling sandbags to protect the hospital and other threatened buildings around the flood-plague city of 5,000.
Many communities in southeast Saskatchewan and western Manitoba have been battling flooding over the past few days after torrential rain fell on the weekend. Melville got over 120 millimetres.
Roads, bridges and culverts have been washed away, crops are ruined and the basements of hundreds of homes in the area have been filled with rainwater and sewage.
Walter Streelasky, the mayor of Melville, said it's been a struggle to keep the flood waters at bay.
"We've got water that's creeping in around our hospital, so we're taking no chances and a full-scale evacuation is on, he said. "We've got a tremendous amount of volunteers sandbagging and doing all these things."
Streelasky says he regrets having to move patients, but he's glad people are there to help.
The Red Cross is on its way, but Streelasky says they could also use more volunteers for sandbagging and to help out at the rink.
Meanwhile, the city is keeping a careful eye on a berm at a reservoir. Streelasky said there is a concern the berm may have been "compromised", although he's not sure if it's broken or breached.
An inspection by helicopter will be done today to find out, he said.