The answer would be likely - "it depends".

Water isn't likely to be affected even by high doses of powerful x-ray radiation from an industrial CT machine (orders of magnitude more powerful than a medical x-ray/CT). It could get a bit warm from the absorbed energy, though.

However with the bottle it would depend a lot on what that bottle has been made from. Glass and metal are very unlikely to be affected to any significant degree even by a strong x-ray source. Plastic - would depend on the dose (time & energy) and what kind of plastic are we talking about. Some could start decomposing/breaking down under the intense x-ray radiation and possibly leach some nasty stuff into the water.

That is very unlikely to happen with a low energy medical x-ray and one-shot exposure, though. However, if you leave a plastic bottle inside of an industrial CT-machine during a multiple hour scan using a high energy beam (e.g. because you are scanning an engine piece made out of metal), there I would be quite careful because who knows how the plastic could react.

And finally, as mentioned by others - it is not enough to be "in the vicinity" for the bottle to be affected by the rays. It would need to be directly in the path of the beam from the x-ray source (or some reflection). X-rays are very directional, the same (or even more so, given it is a shorter wavelength) as light.

Given how well the x-ray machines are shielded and enclosed to avoid accidentally exposing the operators, if your bottle outside of the machine got damaged by x-rays then you would have much much worse problems to care about than some stuff possibly leaching into water ...