Why does water ripple when you throw in a stone?

When the stone hits the water some energy is transferred to the water. Also a volume of water equal to the size of the stone is displaced. Water can not be compressed so the displaced water is forced up, this is the ripple above the level of the water. The energy of the moving stone determines the size. The secondary ripples are a result of the water rushing back in to fill the hole in the water to stone and outward moving ripples left behind. Often you can see a drop of water be ejected when the water rushing in collides. When it falls it will start a new wave train, much smaller then the original. The ripples then are a result of dissipating energy and displaced water.