General manager Tim Barke said the company was frustrated it had the bookings but not the conditions to operate.
"It's been quite a few years since the last time we were off for anywhere near that long," Mr Barke said.
"It's an unusual event having such cold weather for so long.
"It's frustrating when you have the numbers, but it's great having it back open."
Mr Barke said although the ice posed no danger to the boats, the issue was if "there's a problem and we have to clamber out on the rocks".
The company had been waiting for temperatures to rise and for the ice to clear. Both those wishes were granted with the recent rain, which had caused a "flushing effect" and last Friday rafting was able to resume.
He said the water temperature was reported to be -6degC during the freeze and the only reason the river was not frozen solid was due to the flow.
Queenstown Rafting also operated on the Kawarau River and that side of the business was not affected.
Because of the Shotover River's steeper descent, it was popular with "more adventurous" types and there was now a backlog of such people waiting to experience the thrill.
"At this time of year, it's obviously not the busiest time of year for rafting, but it [the closure] does still have an impact because, as the skiers come in for the holidays, it does pick up.
"Luckily, people decided to go on the Kawarau," he said, but he acknowledged the company had missed out on those solely wanting to raft on the Shotover River.
Queenstown Lakes district harbourmaster Marty Black told the Otago Daily Times earlier in the month he had not seen similar conditions for more than 20 years.
Consecutive frosts had not allowed the ice to break free and float downstream.
Shotover Jet and Skippers Canyon Jet were also forced to suspend operations for over a week.
