A photon doesn't transfer part of its energy to water. Either it is absorbed or it is not. The energy is always $E=h\nu$.
A photon doesn't transfer part of its momentum to the water either. If it is absorbed, it transfers all its momentum to an electron of course.
If not, then there are several explanations about what happens and none of them are particularly enlightening. One is the microscopic view, put forth by Mark in the comments below, that the photon is traveling in mostly empty space, punctuated every now and then by a charged particle, and so its momentum doesn't change at all.
This is technically the most correct, but in my opinion not much use if you are looking at macroscopic scales. In that case, we have the Abraham-Minkowski controversy about whether the photon's momentum is higher or lower in a medium. Steve Barnett purports to have solved this controversy in a 2010 paper, as mentioned in the Wikipedia article, and I find that paper easily readable and enlightening. According to Barnett, the Abraham momentum, $P=h\nu/cn$, corresponds to the kinetic momentum of the photon (which is the momentum one usually thinks of when considering a macroscopic body in motion); and the Minkowski momentum, $P=nh\nu/c$, is the canonical momentum (which is defined as Planck's constant divided by the de Broglie wavelength of the body).
The answer is really that "the momentum" of a photon in a medium is not a well-defined concept, so you need to specify what you are talking about.
Working mostly with plane waves myself, I prefer to say $\vec{p}=\hbar\vec{k}$ (which indeed grows by a factor of $n$ in a medium) since this allows me to intuitively explain several other phenomena in terms of conservation of momentum. I will freely admit that this is a gross oversimplification, and also not intuitive in the sense that there is no good explanation why the photon's momentum should be higher, only the unsatisfying mathematical explanation that since the speed of light is "effectively" lower in water, the momentum is "effectively" higher.