Photo would certainly help sort things out. What colours are the 3 wires on the fan? There is a standard colour coding for DC circuits, but you never know these days. It's 12VDC so to run the fan you really only need 2 wires, + & -. The 3rd wire is, as already mentioned, either speed control (requiring additional external circuitry) or for the LEDs.
If you have a 9 volt battery kicking around, it should be easy to find out which are your +- leads. You'll need to cut off the molex connector & strip the wires, or remove the pins. With a jewellers screwdriver, you can generally push the pin out of a molex connector. They have a metal tab that locks the pin in place. Touch the wires to the 9V battery terminals & see in which configuration the fan spins up. Might even light up the LED lights. The fan should run with 9 volts, or at least try to once you get the polarity right. It may even run in either direction if it's reversible. To replace the molex & have a simple interface rather than soldering etc, an adapter as shown in the link below will come in handy in the future. Allows you to adapt your fan wiring to most any wall wart with the standard DC pin connector. Your local electronic supplier may have some of these in stock.
http://www.ebay.ca/itm/DC12V-Power-P...item259ceb4652
I have a bunch of them to adapt my DIY LED strips.
With respect to the LEDs being waterproof, I doubt your fan itself is waterproof either, being designed for a computer (dry environment). The solder connections will all be relatively exposed unless the fan is rated as being water proof or water resistant. Best to keep it all away from a humid environment. Not a big deal with regard to personal safety with 12VDC, but over the long term, exposed to moisture or excess humidity, the various solder connections will corrode. Having said that, I've used standard 12 volt fans in DIY lights over my tank for years without issue.