The unceasing impact of intense sunlight on earth constitutes a continuous source of energy fueling countless natural processes. On a molecular level, the energy contained in the electromagnetic radiation is transferred through photochemical processes into chemical or thermal energy. In the course of such processes, photo-excitations promote molecules into thermally inaccessible excited states. This induces adaptations of their molecular geometry according to the properties of the excited state. Decay processes towards energetically lower lying states in transient molecular geometries result in the formation of excited state relaxation pathways. The photo-chemical relaxation mechanisms depend on the studied system itself, the interactions with its chemical environment and the character of the involved states. This thesis focuses on systems in which photo-induced deprotonation processes occur at specific atomic sites. To detect these excited-state proton dynamics at the affected atoms, a local probe of molecular electronic structure is required. Therefore, site-selective and orbital-specific K-edge soft X-ray spectroscopy techniques are used here to detect photo-induced proton dynamics in gaseous and liquid sample environments. The protonation of nitrogen (N) sites in organic molecules and the oxygen (O) atom in the water molecule are probed locally through transitions between 1s orbitals and the p-derived molecular valence electronic structure. The used techniques are X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). Both yield access to the unoccupied local valence electronic structure, whereas the latter additionally probes occupied states. We apply these probes in optical pump X-ray probe experiments to investigate valence excited-state proton transfer capabilities of aqueous 2-thiopyridone. A characteristic shift of N K-edge X-ray absorption resonances as well as a distinct X-ray emission line are established by us as spectral fingerprints of N deprotonation in the system. We utilize them to identify photo-induced N deprotonation of 2-thiopyridone on femtosecond timescales, in optical pump N K-edge RIXS probe measurements. We further establish excited state proton transfer mechanisms on picosecond and nanosecond timescales along the dominant relaxation pathways of 2-thiopyridone using transient N K-edge XAS. Despite being an excellent probe mechanism for valence excited-state proton dynamics, the K-edge core-excitation itself also disturbs the electronic structure at specific sites of a molecule. The rapid reaction of protons to 1s photo-excitations can yield directional structural distortions within the femtosecond core-excited state lifetime. These directional proton dynamics can change the energetic separation of eigenstates of the system and alter probabilities for radiative decay between them. Both effects yield spectral signatures of the dynamics in RIXS spectra. Using these signatures of RIXS transitions into electronically excited states, we investigate proton dynamics induced by N K-edge excitation in the amino-acid histidine. The minor core-excited state dynamics of histidine in basic and neutral chemical environments allow us to establish XAS and RIXS spectral signatures of different N protonation states at its imidazole N sites. Based on these signatures, we identify an excitation-site-independent N-H dissociation for N K-edge excitation under acidic conditions. Such directional structural deformations, induced by core-excitations, also make proton dynamics in electronic ground states accessible through RIXS transitions into vibrationally excited states. In that context, we interpret high resolution RIXS spectra of the water molecule for three O K-edge resonances based on quantum-chemical wave packet propagation simulations. We show that highly oriented ground state vibrational modes of coupled nuclear motion can be populated through RIXS processes by preparation of core-excited state nuclear wave packets with the same directionality. Based on that, we analytically derive the possibility to extract one-dimensional directional cuts through potential energy surfaces of molecular systems from the corresponding RIXS spectra. We further verify this concept through the extraction of the gas-phase water ground state potential along three coordinates from experimental data in comparison to quantum-chemical simulations of the potential energy surface. This thesis also contains contributions to instrumentation development for investigations of photo-induced molecular dynamics at high brilliance X-ray light sources. We characterize the setup used for the transient valence-excited state XAS measurements of 2-thiopyridone. Therein, a sub-micrometer thin liquid sample environment is established employing in-vacuum flat-jet technology, which enables a transmission experimental geometry. In combination with a MHz-laser system, we achieve a high detection sensitivity for photo-induced X-ray absorption changes. Additionally, we present conceptual improvements for temporal X-ray optical cross-correlation techniques based on transient changes of multilayer optical properties, which are crucial for the realization of femtosecond time-resolved studies at synchrotrons and free-electron lasers.