When a photon passes from the vacuum to a medium such as water, a polariton forms in the water which carries the energy from the photon at a slower speed through the medium. The polariton being essentially a dipole moment propagating through the medium.
So what happened to the photon? Has it been absorbed? Where has it been absorbed into? Has it been absorbed into an elastic potential between charged particles in the medium? In that case, is it the potential between a nucleus and a bound electron, or is the potential between charges in separate atoms? Or am I totally off base?