Due to escalating pollution, the world's clean water supplies are becoming seriously endangered. One of the novel promising methods in water cleaning is cavitation, where a sudden decrease in pressure triggers the formation of vapor and gas bubbles in a liquid medium. Fast and aggressive bubble implosions cause extreme physical-chemical conditions which inactivate bacteria and other contaminants. Despite an extensive research of cavitation, the exact mode of action on bacteria is not known. In doctoral dissertation we compare the effect of hydrodynamic and acoustic cavitation on lipid vesicles, spheroplasts and bacterial cells to the effect of various physio-chemical and mechanical stressors. Further, we evaluate the contribution of the individual cell wall layers on the resistance to cavitation. We show that peptidoglycan layer has the most important effect on cavitation resistance. For fundamental understanding of cavitation, we downscaled the cavitation phenomena to a single micrometer sized cavitation bubble and individual bacterial cell by developing a new method that delivers nanoscale spatial and temporal energy quantum to mechanically remove and destroy individual bacterial cells. The cavitation microbubble had an effect on bacterial cell when it was in proximity of the bubble. Numerical simulations enabled calculation of microbubble evolution and mechanical loads on bacterial cells and allow estimation of threshold values for wall shear stress and hydrodynamic force required for bacterial detachment and destruction. The new results will enable progress and development of cavitation technology towards more efficient and chemical free processes of water treatment.