Sound affects the medium it propagates through and studies on biological systems have shown various properties arising from this phenomenon. As a compressible media and a “collective mirror”, water is influenced by all internal and external influences, changing its molecular structure accordingly. The water molecular structure and its changes can be observed as a whole by measuring its electromagnetic (EMG) spectrum. Using near-infrared spectroscopy and aquaphotomics, this pilot study aimed to better describe and understand the sound-water interaction. Results on purified and mineral waters reported similar effects from the applied 432 Hz and 440 Hz frequency sound, where significant reduction in spectral variations and increased stability in water were shown after the sound perturbation. In general, the sound rearranged the initial water molecular conformations, changing the samples’ properties by increasing strongly bound, ice-like water and decreasing small water clusters and solvation shells. Even though there was only 8 Hz difference in applied sound frequencies, the change of absorbance at water absorbance bands was specific for each frequency and also water-type-dependent. This also means that sound could be effectively used as a perturbation tool together with spectroscopy to identify the type of bio, or aqueous, samples being tested, as well as to identify and even change water functionality.