When the PWC starts it's motion it is just floating on the water. After a short amount of accelleration the PWC will become "on step" or begin hydroplaning, which means the majority of the vehicle is traveling above the water. The effect of hydroplaning is that the effective friction from the water is greatly decreased(there is less surface area contact between the two bodies). Since more of the PWC is above the water the drag is increased. But, since air is less resistant to motion than water, the overall frictional force is decreased.
This can best be seen by the "flying boat". that uses aerodynamic lift to hold the majority of the boat above water.