Disclosed is a pedal drive system for use with a watercraft that facilitates propelling of the watercraft. The pedal drive system of the present invention is placed through an opening in the bottom of the watercraft and affixed to the body of the watercraft. The propeller is then attached to a drive shaft. The user provides mechanical input (e.g., rotational force) by rotating pedals of a pedal arrangement of the pedal drive system. The rotational force is transferred from the drive assembly through the gears to the drive shafts that rotates the propeller, thus driving the watercraft forward as well as backward.