Understanding the bacterial dynamics in cooling towers is imperative for the assessment of disinfection efficiency and management of microbial risks linked to aerosol formation. The objective of this study was to evaluate the impact of feed water on the cooling water bacterial microbiome and investigate the survival ability of its members when exposed to continuous chlorine disinfection. Water from an industrial cooling water system (2600 m/h) was collected over a 5-month period at 3 locations along the feed water line and 3 locations in the cooling tower. ATP measurements suggested that the average ATP-per-cell in the cooling tower evolved independently from the average ATP-per-cell in the feed water. Flow cytometry and 16S rRNA gene amplicon sequencing were then combined to quantify the bacterial dynamics in the whole system. A mass balance based equation was established to determine net growth and net decay of the cooling tower bacterial communities in order to evaluate the impact of continuous chlorination (0.35-0.41 mg Cl/L residual chlorine). The results indicated that cooling tower main community members were determined by the input feed water microbiome and the bacterial community structure was further shaped by varying decay rates of the microorganisms. Notably, the order Obscuribacterales showed to be growing in the cooling tower in the presence of residual chlorine up to 0.4 mg Cl/L, with a recurrent net growth of 260 ± 95%, taking into account the impact of the concentration factor. This conclusion was only possible thanks to the systematic analysis described in this paper and generates discussion about the resistance of Obscuribacterales to residual chlorine. The described mass balance approach provides a high level of understanding on bacterial dynamics and should be considered for future characterization studies of cooling towers in which accurate investigation of microbiome changes is essential.