In this study, an environmental sampling campaign was conducted to detect internalized E. coli and C. jejuni bacteria in zooplankton and amoebae samples collected at various stages of three water treatment plants in Amsterdam, the Netherlands. Eight sampling locations were selected and sampling was performed twice, at a two-week interval, at each location. Chlorination was used to inactivate free (external) bacteria in the concentrated zooplankton samples and sonication was used to disrupt zooplankton organisms in order to release and recover internalized bacteria. Zooplankton enumeration was performed by microscopy. No internalized E. coli or C. jejuni bacteria were recovered from all of the samples analyzed. The occurrence of internalized E. coli or C. jejuni bacteria in drinking water was estimated to be lower than one internalized bacteria in 10⁵ zooplankton organisms, as derived from the detection limit of the sampling campaign. By using the QMRA approach and the Beta-Poisson model, a risk of infection of less than 9.2E-6 and 5.9E-5 was estimated for internalized E. coli and C. jejuni in drinking water, respectively. This study remains preliminary due to the limited number of samples taken at each location.