Business owners along East Main Street arrived Friday morning to find shops submerged under several inches of water.
The water took them completely by surprise and some aren't sure how they'll be able to recover.
Deb Wheaton owns Gluten Free Prairie Bakery.
She says, "It was like a waterfall in our brand new bakery. We just had a $30,000 piece of equipment delivered yesterday."
Wheaton showed NBC Montana inside the flooded bakery. The water was almost 6 inches deep. Wheaton pointed out broken equipment and the basement with 10-foot high ceilings, filled with water.
Wheaton told us, "We're going to pump as much water out as we can today."
Her husband Rick Wheaton added, "We're hoping that the city can get the front lowered so the water stops seeping into the building."
The Wheatons co-own the bakery along with their son, but they say removing the water is the least of their worries.
"A lot of us realized that we don't have the proper flood insurance," said Deb Wheaton. "We just never considered this."
No insurance means the bakery, which hasn't even officially opened yet, could become a total loss, putting its future into jeopardy. It's a problem shared by many business owners in the area.
Tom Petrick owns L & F Foods two doors down from the Wheatons' bakery. "According to my insurance we're not covered at this time," he revealed.
Petrick spent the day trying to save anything he could. All the refrigerated foods have to be relocated.
"I just feel for everybody who has the same problem," Petrick said. "We're just one of many businesses going through this."
For now, Rick Wheaton is tackling his problems one at a time, but regrets more preventive measures weren't taken by the city.
"We wish Manhattan had been a little more prepared for this. I know it caught them off-guard as well. Now we have to deal with what we have," he said.
Over three hours after flood waters were first being removed from Gluten Free Prairie Bakery, crews continued to push that water into drains.