Flow cytometry represents an important tool in environmental biology, and especially in cellular biology, through its ability to distinguish among different physiological states (viable, latent and non-viable). Flow cytometry combined with fluorescent markers, such as propidium iodide and ethidium bromide allows to perform rapid measurements on individual cells and also simultaneous measurements of multiple cellular parameters, both structural and functional. The aim of this paper was to investigate the influence of the electromagnetic field on the morpho-physiological parameters of some bacterial strains cells isolated from wastewater, assessed through flow cytometry. In this respect, a number of 10 bacterial strains isolated from wastewater (E. coli, Salmonella sp., Enterobacter sp., Citrobacter sp., Klebsiella sp. and Enterococcus sp.) were exposed to an electromagnetic field (50Hz electric field at different voltages) for 24 hours, at 37°C. Both samples, the ones exposed to electromagnetic field and blank samples (unexposed) were assessed by flow cytometry technique. Two possible mechanism of action have been tracked, i.e. the efflux pumps activity (fluorescence markerEthidium Bromide) and permeabilisation of cellular layers (fluorescence marker -Propidium Iodide). Both mechanisms of action have been identified, from slightly to significant modifications, as compared to untreated controls, quantified as ΔMFI (median of fluorescence intensity). Conclusion: Our results suggest that flow cytometry could be used for the real-time evaluation of the influence of different electromagnetic fields on the aquatic microbiota, the obtained results being of great interest for the development of technological solution with increased efficiency in the (waste)water treatment.