Objective To assess whether bacterial colonisation in a power-driven water flosser can be prevented. Materials and methods Twenty-four patients undergoing supportive periodontal treatment used 2 power-driven water flossers [Sonicare AirFloss (SAF), AirFloss Ultra (SAFU)] for 12 weeks each as follows: (a) with bottled water (BW); (b) with BW and cleaning the device extra-orally twice per week with chlorhexidine gluconate or (c) essential-oil-based (EO) mouth-rinse; (d) with EO only. Water-jet samples were taken after 6 and 12 weeks with the used nozzle and after exchanging to a brand-new nozzle. After 12 weeks, all devices underwent an intensive cleaning procedure. Samples were analysed by PCR-based method for cariogenic and periodontal pathogens and culture for staphylococci, aerobe gram-negative bacteria, and Candida sp. Results Contamination of SAF/SAFU with Streptococcus mutans was found in > 95% of the samples; periodontal pathogens and aerobe gram-negative bacteria were detected in 19-56% of the samples, while Staphylococcus aureus and Candida sp. were identified only in few samples. Contamination rate was basically unaffected by time-point, device, or way of use. Further, exchanging the nozzle did not prevent transmission of a contaminated water-jet, but the intensive cleaning reduced most of the pathogens significantly, except of S. mutans. Conclusion Neither a specific way of use nor exchanging the nozzle prevented bacterial colonisation and transmission of biofilm components via the water-jet of SAF/SAFU.