One‐dimensional flow experiments on biological clogging were carried out by biostimulating columns packed with glass beads, sterilized, and inoculated with toluene‐utilizing bacteria. Biostimulation consisted of continuously injecting toluene at four concentrations (3.0 ± 0.9, 6.1 ± 0.8, 8.7 ± 1.6, and 11.3 ± 0.8 mg/L). The results of column flow experiments indicated that a threshold concentration of toluene exists below which the total biomass in the column can be kept at a steady‐state level. The column cores were extruded and segmented to determine the biomass distribution throughout the column at clogging. Clogging resulted in a significant buildup of filamentous bacteria close to the inlet end. Based on the nucleotide sequence of 16S rRNA genes, the dominant filamentous bacteria were identified as Nocardia farcinica. A 235‐d column experiment demonstrated that the clogging near injection points can be controlled by keeping the influent concentration of toluene below the threshold.