It is well documented that invertebrates can ingest and transport pathogenic bacteria, thus protecting the bacteria against disinfection in the laboratory. However, the risk assessment of and corresponding disinfection methods for natural invertebrate-internalized bacteria in biological activated carbon (BAC) filtration systems remain poorly understood. In this study, the risk of natural invertebrate-internalized bacteria was comprehensively assessed and methods to inactivate these bacteria were compared in a pilot-scale BAC filtration column study lasting one year. Seven groups of invertebrates dominated by rotifers and crustaceans were detected in the filtration column, five of which were collected for quantitative/qualitative identification of the bacteria they internalized. The community composition of internalized bacteria was analyzed via polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) coupled with sequence analysis of 16S rRNA gene fragments. Results showed that the average numbers of internalized bacteria per organism ranged from 160 to 6000, which increased exponentially with invertebrate body length. Some of the invertebrate-internalized bacteria were identified as opportunistic human pathogens, but no direct human pathogens were detected. A model was developed to calculate the residual bacteria concentration. Using this model, it was determined that an average of 800–100,000 CFU/m3 internalized bacteria would be protected and then released into the distribution mains after chlorination of 50 mg/L·min, with rotifers and copepods the dominant sources. Ozonation was more effective than both chlorination and UV radiation for inactivating the invertebrate-internalized bacteria.