The Life Education Trust - Canterbury charity was able to hold the Corporate Race but the Community Race was "sadly called off".
A spokesperson said the rain and high tide caused the river to rapidly rise meaning volunteers couldn't hold on to the netting used to collect the ducks.
During the Corporate Race, one duck was even seen sprouting a remote-controlled propellor and taking the lead.
"There were surprises in store for the Corporate Race when one duck sprouted a remote controlled propellor and took the lead," a Life Education Trust spokesperson said.
"Race rules are very strict about added propulsion so while we love the ingenuity from Stephen Parkinson Orthopaedics, it's a penalty for you until next year.
"The Community Race was sadly called off. We had to make the call to put their safety and our responsibility to remove every duck from the river first. Instead, Harold the Giraffe was on hand to immediately draw three winners at random from the public entrants.
"A tremendous thank you to all who ventured out in the rain to support the Duck Race."
The three winners of the Community Race drawn at random were:
1st: Zhuojiong Ma - duck 106
2nd: Grayson Mynott - duck 1519
3rd: Mark Adams - duck 1502
"In six years we have never had rain. To have our community turn up anyway despite this was just incredible. To our sponsors and their staff who came along we can't thank you enough. To MC Angus and More FM we are so grateful! A big thank you to Melissa and the team from Rotary New Horizons who braved the river as our waders, we applaud you."
