A foot-operated propulsion system for small watercraft, such as kayaks. The propulsion system includes a pedal assembly that controls motion of a fluke fin that is submerged beneath the waters surface. The pedal assembly is located in the bow of the watercraft and the paddler works the pedals with his feet. Operating the pedal assembly causes a force to be transmitted to a drive unit located in the stern of the craft, which then controls movement of linkages in the fluke assembly, to force the submerged fluke fin to swing upward and downward, emulating the motion of flukes on a whale, and thereby propelling the watercraft along the surface of the water.