Raw 16S rRNA gene amplicon sequencing file of the DNA extracted from a full-scale cooling tower water samples during a 5-month period. The files were used to investigate the microbial dynamics and assess the growth or decay of the bacterial community members in the cooling system, when combined to flow cytometry analyses. The method allows to identify microorganisms that demonstrate higher resistance to disinfection. In general, the study contributes to a better knowledge of cooling towers and of the impact of continuous chlorination on the overall microbial community.