The flight instructor reported that during the water takeoff to the north, in the floatplane, he noticed a jet boat that was operating about 1,000 ft east of the floatplane. The boat was traveling generally in the same direction and diverging from the area which they had planned to takeoff. During the takeoff run, the boat abruptly altered its course and began to converge upon the floatplane’s takeoff path. The flight instructor told the pilot receiving instruction to turn left, as he retarded the throttle to the idle position in an attempt to avoid the boat. The boat subsequently collided with the right side of the floatplane substantially damaging the right-side empennage and stabilizer. Just before the boat collided with the floatplane, the pilot observed that the boat operator was turned completely towards the rear of the boat. The pilot reported that there were no preaccident mechanical failures or malfunctions with the airplane that would have precluded normal operation.