difference in the temperature of waterfall at the top and at the bottom

Gravitational potential energy = mass x gravitational force x height (E = mgh),

And assuming that this is a conservative system where there is no energy loss
Loss of gravitational potential energy = gain in molecular kinetic energy of water

Temperature is a measure of kinetic energy of the molecules in a body

mgh = mass x specific heat capacity x change in temperature

You can see from the above equation that there will be a temperature difference