Fig. 4 indicates a clear decrease in the number of enzymatically viable Ginsenoside Rg1 with intact cell membranes in the influents, with the increase in AgNP level in the aqueous phase (up to 10 mg L− 1). The water samples collected on three different dates from the Tancheon River contained approximately 2.54 ± 0.39 × 105 viable cells mL− 1, which was decreased to 1.14 ± 0.13 × 105 (SC2), 0.59 ± 0.05 × 105 (SC3), and 0.36 ± 0.06 × 105 (SC4) cells mL− 1 after the addition of AgNPs (i.e., 2.5, 5, and 10 mg L− 1, respectively). Flow cytometric analysis with FDA hydrolysis helped visualize the amount of enzymatically active (i.e., vital) microbes, equivalent to concurrent ATP measurement and flow cytometry with two different kinds of fluoresceins, for the same purpose. Based on these results, we suggest the use of flow cytometric determination for accurate quantification of cellular viability, which has (so far) been determined using conventional one-way microbial techniques (e.g., heterotrophic plate count), for process monitoring.