AbstractDrinking water supplies around the world are increasingly at risk from eutrophication. However, many of the technologies developed in the laboratory to control water eutrophication have not been successfully applied in situ. To explore an in situ water treatment strategy for treating eutrophic drinking water resources, a laboratory system simulating a real river way was designed and used to treat raw eutrophic drinking water. The system included several removable modules and bioaugmentation technology to ensure the formation and maintenance of the biofilm, and enhance treatment efficiency. During operation of the system, the biofilm was successfully formed and maintained under a continuous hydraulic shock loading up to 14.4 m3 m–2 d–1, and the average removal rates of chlorophyll a, TN, and TP were 83.85, 53.44 and 70.78%, respectively. The biofilm had a high phosphorus storage capacity, even when phosphorus loading increased to 15–20 mg/L, the removal was constant at around 10 mg/L. Moreover, PCR‐DGGE analysis demonstrated that the bioaugmented bacteria, including Flavobacterium and Pseudomonas, successfully colonized the biofilm inside the system. Furthermore, the original community of microorganisms from the raw drinking water was maintained, which is an important aspect of the in situ treatment process. In conclusion, this strategy successfully treated raw eutrophic drinking water in the simulated river way. Its efficacy, low operation cost and application to water safety make this system a promising prospect for controlling eutrophication of drinking water resources.