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Hi, just stumbled over your project and I know you either found a way to waterproof your motor or you have put this project on the shelf by now, but just a tip..
all the motors out there use insulated wire in their coil, but brushed motors are not very good choise in underwater motors, but on the other hand, brushless motors are by design completely watertight, as it has no open electrical surfaces, the only "weak spot" is the connection between the coil wiring and the motor wiring, but in fresh water you should see no problem there as well..
But with a brushless motor you will get a 3phase AC output, and you will most likely need to get a converter to DC.

annyway, good luck :)