Good point, I was not considering drag and now I have realized that turbulence is another issue to deal with.
No, it isn't. As I said I'm not a physicist, nor an engineer, but that does not mean that I'm a fool!
Anyway, thanks for the answers and if someone has any other remarks then...
Wikipedia says: "If the object is much denser than the fluid, then B (the buoyancy force) approaches zero and the object's upward acceleration is approximately −g, i.e. it is accelerated downward due to gravity as if the fluid were not present"
So buoyancy isn't reducing the energy available...
You are right, in this setup water has no purpose, but the drawing is only one part of a system in which water is necessary. I tried to simplify, this is the only part I'm having troubles with.
Suppose that we have a tower with two compartments. The upper one is filled with mercury and the bottom one with water. The floor can be opened (and so the compartments are abolished), and mercury could flow down to the bottom of the tower. I have calculated the potential energies of the two...