A Raman spectroscopic study of Cu2ZnSnS4 (CZTS) nanocrystals (NCs) produced by a “green” synthesis in aqueous solutions is reported. Size-selected CZTS NCs reveal phonon confinement that manifests itself in an upward shift of the main phonon peak by about 3–4 cm−1 by varying the NC diameter from 3 to 2 nm. A non-monotonous shift and narrowing of the main peak are attributed to the special shape of the phonon dispersion in this material. Moreover, the method of sample preparation, the nature of the supporting substrate and the photoexcitation regime are found to crucially influence the Raman spectra of the CZTS samples. Particularly, the possible oxidation and hydrolysis of CZTS NCs with the concomitant formation of a Cu–S phase are systematically investigated. The nature of the film support is found to strongly affect the amount of admixture copper sulfide phases with the Cu2−xS/CuS content being the highest for oxidized silicon and glass and notably lower for ITO and even less for gold supports. The effect is assumed to originate from the different hydrophilicity of the supporting surfaces, resulting in a different morphology and surface area of the NC film exposed to the atmosphere, as well as the degree of the NC oxidation/hydrolysis. The amount of copper sulfide increases with the laser power. This effect is interpreted as a result of photochemical/photocatalytic transformations of the CZTS NCs.