While atmospheric pressure plasma sources are emerging as potentially innovative instruments in medicine, some aspects of the interaction between plasma and biological substrates remain unclear. The high diversity in both sources and applications in the literature, and the lack of a systematic testing protocol, has resulted in a wide variety of devices that cannot be efficiently compared with one another. In this work, an integrated benchmark involving physical, chemical, and biological diagnostics is proposed. The setup is designed to be stable and fixed, while remaining adaptable to different sources. Three different sources, for a total of five configurations, are compared, demonstrating the possibility of obtaining multimodal data. Comparing the biological effects in terms of E. coli abatement between direct and indirect treatments allowed for the exclusion of short-timescale species and phenomena to have a key role in the abatement. The chemical characterisation describes the equilibrium of reactive oxygen and nitrogen species in treated samples, whose presence in the water has been found to be coherent with the plasma operating gas and the nitrogen vibrational temperatures. Nitrate, nitrite and peroxide are excluded from having an autonomous role in the inactivation biochemistry, suggesting the presence of a synergistic effect.