Water isn't a big (chemical) issue but oxygen certainly is. A primary reason is that photoexcited organic molecules often end up in a longish-lived triplet excited state
, which can efficiently photosensitize
production of singlet oxygen
. Singlet oxygen is basically a molecular wrecking ball that tears apart organic matter... often including the original molecule that generated it. Actually, despite being a strong oxidant, oxygen - being a ground state triplet - is kinetically stable. Strictly speaking, it can't react with organic molecules, which most of the time are ground state singlets. Such reaction events are formally spin forbidden. When either organic molecules are photoexcited to their triplet states, that kinetic bottleneck disappears. Oxidation events between organic molecules and substrates are formally always due to thermal or photophysical activation of an organic substrate to its excited triplet or oxygen to its excited singlet. That those energy gaps are so large (and the probability of thermal activation is correspondingly low) is the only reason stable organic molecules can exist in an oxygenated atmosphere at room temperature.
Unless studying generation of singlet oxygen is the primary goal, experimentalists usually take great pains to deaerate samples prior to doing sophisticated spectroscopy experiments.
Water does have strong intermolecular interactions and can greatly affect rates of photophysical events. So it is frequently preferable to do spectroscopic measurements in dry, nonpolar (and deoxygenated) solvents ... but it all depends on what you're trying to do. Sometimes your substrate is intended to be dissolved in water, so in that case, water it is!