The physicochemical properties of van der Waals (vdW) heterostructures are driven by the delicate interactions between the individual layers in a multilayer stack. While addressing the monolayers of different compositions in the multilayer is feasible, exploring the intrinsic properties of the monolayers of the same composition within a multilayer is extremely challenging. This becomes of utmost importance in energy conversion and storage concepts based on layered vdW materials. For example, the charge distribution on the individual layers can be determined, and the behavior can be disentangled. We introduce sulfur isotope labeling as a powerful tool for separately addressing monolayers in vdW heterostructures composed of transition metal disulfides. Using chemical vapor deposition (CVD), we prepared monolayers of MoS2 using natural sulfur (NatS) and 34sulfur (34S) as precursors. Artificial bilayers were then prepared by transferring Mo34S2 onto MoNatS2. Thanks to the different masses of NatS and 34S, we were able to disentangle the spectral fingerprints of phonons and excitons in the two layers using Raman and photoluminescence microspectroscopy. Also, the charge distribution on the individual layers was revealed through Raman spectra analysis. Our work thus provides a different perspective for understanding the functionalities and optical properties of smart architecture based on transition metal chalcogenides.