It happened near the steep canyon by the Bill Healy Bridge.
Bend Fire Battallion Chief Bob Madden says this is a popular and dangerous part of the river.
"A lot of local experiened kayakers do a lot of kayaking there, but someone inexperienced or ill equipped would have a tough time. We've had fatalities there. Know what's below you .. don't take anything for granted. There is some real tricky water on the Deschutes."
Three kayakers were involved. One got to shore and alerted authorities about the two others.
They were eventually rescued, but crews warn kayakers to be aware of the difficulty of the terrain you're traveling.