The development of alternative techniques to efficiently inactivate bacterial suspensions is crucial to prevent transmission of waterborne illness, particularly when commonly used techniques such as heating, filtration, chlorination, or ultraviolet treatment are not practical or feasible. We examine the effect of MHz-order acoustic wave irradiation in the form of surface acoustic waves (SAWs) on Gram-positive (Escherichia coli) and Gram-negative (Brevibacillus borstelensis and Staphylococcus aureus) bacteria suspended in water droplets. A significant increase in the relative bacterial load reduction of colony-forming units (up to 74%) can be achieved by either increasing (1) the excitation power, or, (2) the acoustic treatment duration, which we attributed to the effect of the acoustic radiation force exerted on the bacteria. Consequently, by increasing the maximum pressure amplitude via a hybrid modulation scheme involving a combination of amplitude and pulse-width modulation, we observe that the bacterial inactivation efficiency can be further increased by approximately 14%. By combining this scalable acoustic-based bacterial inactivation platform with plasma-activated water, a 100% reduction in E. coli is observed in less than 10 mins, therefore demonstrating the potential of the synergistic effects of MHz-order acoustic irradiation and plasma-activated water as an efficient strategy for water decontamination.