Accurate comparison of flow cytometric data requires an understanding of how the cytometric fingerprint of a sample may vary from instrument to instrument. Key sources of variability include the number, wavelengths, and power of excitation lasers; the number and types of emission detectors; sample-handling systems and options; and whether fixed or dynamic detector voltages are used. To explore this variability, suspensions of three sizes (0.2, 0.5, and 0.8 μm-diameter) of solid, fluorescent, polystyrene beads were prepared. The suspensions were then run on four flow cytometers, keeping instrument settings as consistent as possible. The results are displayed graphically in Figure 3 of the article "Flow cytometry applications in water treatment, distribution, and reuse: A review" (DOI: 10.1016/j.watres.2018.12.016) [1]. This dataset contains the complete FCS files generated from the experimental comparison. In the development and application of flow cytometry to water quality assessment, we recommend data sharing in this manner to enable comprehensive reporting, meaningful comparison of results obtained using different cytometer models, enhanced exploration of data along multiple parameters, and use of acquired data for computational advancements in the field.