You don't have to buy ducks--some companies actually rent them to you so there is no storage concern or big investment initially.
Find a water way, river or ocean where you can host the race--some groups even host the event in a public swimming pool, or they create a water maze for the ducks to ride along to a finish line. The should be some sort of current to make the rubber ducks move to a finish line. Once you have found a viable location, begin your planning strategy.
Create a volunteer base. People need to be available to help coordinate, promote, sell and tag the ducks before the race.
Establish a bookkeeping system for each duck sold. A person "buying" the duck may give it a name but due to duplication of names, you'll need to also assign numbers to the ducks and place them on the rubber duckies with permanent marker pens.
Set prices and establish a sponsorship system. A tittle sponsor such as a radio or TV station may help spread the word about the event. Most individual duck sponsors pay $5-20 for a duck. Corporate sponsors and corporate races may be in the $100/duck range. Title sponsors go up from there and can be in-kind trade.
Get prizes from community. TVs, trips, hotel stays, houseboat rentals and other such items are attractive prizes.
Arrange for charities to become recipients of the prize money. They may draw from their mailing lists and member bases to help sell ducks and spread the word.
Have a finish line and many volunteers to document duck winners.
Some duck derbies allow buyers to keep their sponsored ducks and pick them up after the race. Make sure that you have written rules clearly printed for buyers to see.
Get ready for next year. Duck derbies are infectious. Once you host such an event, the public is eager for its return.
Events are not guaranteed. It is your responsibility to confirm before going.