The flight instructor reported that he and a student pilot were returning to the seaplane base after completing the student pilot’s instructional stage check for a commercial single-engine sea rating. During the final approach for landing, the flight instructor noticed the seaplane’s glide path flown by the student pilot was high and would require most of the waterway to land. The flight instructor took control of the seaplane to correct for the high glide path. After the flight instructor corrected the seaplane’s glide path, the seaplane touched down on the waterway, and the flight instructor applied left rudder control to keep the seaplane centered on the waterway. The seaplane continued to the right and struck a sand bank where it nosed over. The seaplane sustained substantial damage to the left wing spar. The flight instructor reported no preaccident failures or malfunctions with the seaplane that would have precluded normal operations. The flight instructor felt that the touch down attitude was flat resulting in an inadvertent water loop.