This thesis explores ultrafast dynamics in biological and molecular systems using femtosecond X-ray absorption spectroscopy (TRXAS) and several multiphoton absorption schemes. It develops novel TRXAS methodologies using high-harmonic generation in the water window to probe femtosecond proton transfer in aqueous urea, combining experiment with QM/MM simulations to disentangle electronic and nuclear couplings. The findings reveal the critical influence of solvation on biomolecular behaviour. The second part investigates multiphoton absorption, including the response of rhodopsin to the phase control of infrared pulses in murine retina, and the measurement of ETPA cross-sections in organic molecules. A new figure of merit, δ_ETPA, is proposed to standardize ETPA quantification. Rigorous upper bounds are established for molecules such as Styryl 9M and ZnTPP. Overall, the results advance TRXAS methodologies and investigate quantum-enhanced spectroscopy. The work opens new pathways for studying fundamental biomolecular processes and for developing precision tools in ultrafast spectroscopy and quantum optics.