Reusing reclaimed water through drip irrigation offers an effective way to overcome freshwater scarcity. However, biofilm accumulation in the flow channel of drip emitters is the primary obstacle. So far, biofilm development in the emitters remains largely unknown. Here, industrial computed tomography was used to quantify the emitter biofilm developments. Results showed that biofilm typically accumulated in the inlet of the emitter flow channel and decreased toward the flow direction. Biofilm was also typically accumulated in dead areas having low flow velocities, such as edge, corner, and adjacent surface zones in flow channels. The dynamics of the emitter biofilm variation mechanisms were also elucidated. Specifically, particle and nutrient transport appeared to be dominant in shaping the initial biofilm formation (i.e., 5% emitter clogging degree), resulting in biofilm abundant in the inlet of the flow channel. However, it changed the hydraulic conditions in emitter flow channels, increased local water shear stress, which made the biofilm easier to be washed away in the inlet, and caused biofilm to grow faster in the middle and outlet regions of the flow channel at 20% emitter clogging degree. At 50% clogging degree, biofilm in inlet regions grew faster again. Finally, some biofilm control approaches such as water quality management and emitter flow channel structure optimization were proposed. This study provided a better understanding of biofilm formation mechanisms in the emitter flow channels, which is critical for designing appropriate biofilm control technologies and will facilitate the reuse of reclaimed water in agricultural irrigation. Display omitted •The biofilm developments in drip irrigation emitters were visualized and quantified.•The critical regions of biofilm accumulation in the emitter channel were identified.•The dynamics of the emitter biofilm variation mechanisms were elucidated.•Some approaches for controlling the biofilm in the emitter channel were proposed.