Authorities said one person was believed to have died in a building collapse near the town of Jamestown, NBC News reported.
The other two bodies were found along roadways.
The National Weather service said in a statement just after midnight the intensity of the rains had created a "life-threatening situation." About 6.5 inches of rain had fallen around Boulder in 24 hours, the service said.
Numerous buildings have collapsed, but it was unclear how many or if there were any other injuries related to the fallen structures, county spokeswoman Gabbie Boerkircher said.
Mandatory evacuation orders were in place in Jamestown and Fourmile Canyon, officials said.
The Boulder Office of Emergency Management said people in the city of Boulder living in low lying areas should move to higher ground.
In Lyons, north of Boulder, water spilled over the top of five dams, Boerkircher said. Emergency officials were monitoring the dams, which hadn't broken as of early Thursday.
The National Weather Service said the St. Vrain Creek at Lyons was at 8.7 feet Thursday morning. The flood stage is 8.5 feet.
Officials urged residents to stay home and off flooded and sometimes impassible roads. City and county offices, the University of Colorado-Boulder and area schools were closed Thursday.
The university said it relocated more than 400 graduate students and research faculty members from housing units because of flooding and relocated 13 undergraduates from two residence halls, CNN reported.
The National Weather Service said moderate to heavy rain were forecast through Thursday evening and said rainfall rates "in excess of 2 inches per hour" could lead to flash flooding.
The forecast for Boulder area could see a chance of rain through Sunday, NWS said.
The Boulder Daily Camera said Boulder has been listed among Colorado's top flood hazards and was included on a national list of six "disasters waiting to happen" published by Colorado University in 2004.