the bottom of a container of water will have the temperature of the water, so thats not an issue, that would be good enough. water (at least in this context) is excellent at conducting heat. would there be a difference when you measure the bottom, which is plastic or glass or stone or whatever, which is in direct contact with the water you want to measure? but i think water is actually quite intransparent in the infrared. reflections can be minimized by pointing the temp gun at a 90 degree angle directly down into the water. trust me, quantum electrodynamics applies to all wavelengths, that includes infrared, reflections will be minimal at a 90 degrees angle.
but we have to differentiate, im only talking about infrared temp guns that measure the amount of incoming infrared radiation. laser temp guns are completely different, but they are rare and expensive, they measure whatever comes back from the beam, and detect any shift or spread of the wavelength. these are not present in reptile keeping, their advantage is incredible range, you use them to measure surface temperatures of earth from low earth orbit. so i think we are talking about infrared.