Water suppliers aim to achieve microbiological stability throughout their supply system by regular monitoring of water quality. Monitoring temporal biomass dynamics at high frequency is time consuming due to the labor-intensive nature and limitations of conventional, cultivation-based detection methods. The goal of this study was to assess the value of new rapid monitoring methods for quantifying and characterizing dynamic fluctuations in bacterial biomass. Using flow cytometry and two precise enzymatic detection methods, bacterial biomass-related parameters were monitored at three riverbank filtration sites. Additionally, the treatment capacity of an ultrafiltration pilot plant was researched using online flow-cytometry. The results provide insights into microbiological quality of treated water and emphasize the value of rapid, easy and sensitive alternatives to traditional bacterial monitoring techniques.